| Journal article |
- Christian Gusenda; Ana R. Calixto; Joana R. Da Silva; Pedro A. Fernandes; Martin Grininger. "Die Kinetik der Kohlenstoff-Kohlenstoff-Bindungsbildung
in der metazoischen Fettsäure Synthase und ihr Einfluss auf die Produktgenauigkeit". Angewandte Chemie (2025): https://doi.org/10.1002/ange.202412195.
10.1002/ange.202412195
- Christian Gusenda; Ana R. Calixto; Joana R. Da Silva; Pedro A. Fernandes; Martin Grininger. "The Kinetics of Carbon-Carbon
Bond Formation in Metazoan Fatty Acid Synthase and Its Impact on Product Fidelity". Angewandte Chemie International Edition
(2025): https://doi.org/10.1002/anie.202412195.
10.1002/anie.202412195
- Joana R. da Silva; Maria João Ramos; Pedro A. Fernandes. "Elucidating on the quaternary structure of viper venom phospholipase
A2 enzymes in aqueous solution". Biochimie (2025): https://doi.org/10.1016/j.biochi.2024.12.015.
10.1016/j.biochi.2024.12.015
- João P. M. Sousa; Maria J. Ramos; Pedro A. Fernandes. "The Catalytic Mechanism of Decarboxylation of L-DOPA to Dopamine by
Papaver somniferum Aromatic Amino Acid Decarboxylase – A Computational Study". ChemCatChem (2025): https://doi.org/10.1002/cctc.202400762.
10.1002/cctc.202400762
- P. Paiva; E. Ippoliti; P. Carloni; P. A. Fernandes; M. J. Ramos. "Atomistic adsorption of PETase onto large-scale PET 3D-models
that mimic reality". Physical Chemistry Chemical Physics (2025): https://doi.org/10.1039/D4CP03488K.
10.1039/D4CP03488K
- Juliana Castro-Amorim; Alexandre V. Pinto; Ashis K. Mukherjee; Maria J. Ramos; Pedro A. Fernandes. "Beyond Fang's fury: a
computational study of the enzyme–membrane interaction and catalytic pathway of the snake venom phospholipase A2 toxin". Chemical
Science (2025): https://doi.org/10.1039/D4SC06511E.
10.1039/D4SC06511E
- Paiva, Pedro; Correia Teixeira, Luís Miguel; Ren, Wei; Liu, Weidong; Weber, Gert; Morth, Jens Preben; Westh, Peter; et al.
"Unveiling the Enzymatic Pathway of UMG-SP2 Urethanase: Insights into Polyurethane Degradation at the Atomic Level". Chemical
Science (2025): https://doi.org/10.1039/d4sc06688j.
10.1039/d4sc06688j
- Beatriz T. Magalhães; João T. S. Coimbra; Raquel M. Silva; Mariana Ferreira; Rita S. Santos; Paula Gameiro; Nuno F. Azevedo;
Pedro A. Fernandes. "Crosstalk of Nucleic Acid Mimics with Lipid Membranes: A Multifaceted Computational and Experimental
Study". Biochemistry (2024): https://doi.org/10.1021/acs.biochem.4c00349.
10.1021/acs.biochem.4c00349
- João T. S. Coimbra; Antoine Gissler; Emiel Nitor; Kiana Rostamipour; Ana V. Cunha; Maria J. Ramos; Pedro A. Fernandes. "Venomous
Peptides: Molecular Origin of the Toxicity of Snake Venom PLA2-like Peptides". JACS Au (2024): https://doi.org/10.1021/jacsau.4c00646.
10.1021/jacsau.4c00646
- João P. M. Sousa; Maria J. Ramos; Pedro A. Fernandes. "QM/MM Study of the Reaction Mechanism of L-Tyrosine Hydroxylation Catalyzed
by the Enzyme CYP76AD1". The Journal of Physical Chemistry B (2024): https://doi.org/10.1021/acs.jpcb.4c05209.
10.1021/acs.jpcb.4c05209
- Coelho, Maria Miguel; Lima, Rita; Almeida, Ana Sofia; Fernandes, Pedro Alexandrino; Remião, Fernando; Fernandes, Carla; Tiritan,
Maria Elizabeth. Corresponding author: Fernandes, Carla. "Binding studies of promethazine and its metabolites with human serum
albumin by high performance affinity chromatography and molecular docking in the presence of codeine". Analytical and Bioanalytical
Chemistry (2024):
Published
- Ali, Mohd Sajid; Luís M. C. Teixeira; Ramos, Maria João; Fernandes, Pedro Alexandrino; Al-Lohedan, Hamad A.. "Interaction
of major saffron constituent safranal with trypsin: An experimental and computational investigation". International Journal
of Biological Macromolecules (2024): http://dx.doi.org/10.1016/j.ijbiomac.2024.133231.
10.1016/j.ijbiomac.2024.133231
- Pedro Ferreira; Rui P. P. Neves; Filipa P. Miranda; Ana V. Cunha; Remco W. A. Havenith; Maria J. Ramos; Pedro A. Fernandes.
"DszA Catalyzes C–S Bond Cleavage through N5–Hydroperoxyl Formation". Journal of Chemical Information and Modeling
(2024): https://doi.org/10.1021/acs.jcim.4c00301.
10.1021/acs.jcim.4c00301
- Carlos F. M. Silva; Diana C. G. A. Pinto; Pedro A. Fernandes; Artur M. S. Silva. "Evolution of the Quinoline Scaffold for
the Treatment of Leishmaniasis: A Structural Perspective". Pharmaceuticals (2024): https://doi.org/10.3390/ph17030285.
10.3390/ph17030285
- Ana L. Novo de Oliveira; Miguel T. Lacerda; Maria J. Ramos; Pedro A. Fernandes. "Viper Venom Phospholipase A2 Database: The
Structural and Functional Anatomy of a Primary Toxin in Envenomation". Toxins (2024): https://doi.org/10.3390/toxins16020071.
10.3390/toxins16020071
- Carola Jerves; Rui P. P. Neves; Saulo L. da Silva; Maria J. Ramos; Pedro A. Fernandes. "Rate-enhancing PETase mutations determined
through DFT/MM molecular dynamics simulations". New Journal of Chemistry (2024): https://doi.org/10.1039/D3NJ04204A.
10.1039/D3NJ04204A
- Boro, N; Fernandes, PA; Mukherjee, AK. "Computational analysis to comprehend the structure-function properties of fibrinolytic
enzymes from Bacillus spp for their efficient integration into industrial applications". HELIYON (2024): https://www.authenticus.pt/P-010-YST.
10.1016/j.heliyon.2024.e33895
- João T. S. Coimbra; Pedro A. Fernandes; Maria J. Ramos. "Deciphering the Catalytic Mechanism of Virginiamycin B Lyase with
Multiscale Methods and Molecular Dynamics Simulations". Journal of Chemical Information and Modeling (2023): https://doi.org/10.1021/acs.jcim.3c00962.
10.1021/acs.jcim.3c00962
- Juliana Castro-Amorim; Ana Oliveira; Ashis K. Mukherjee; Maria J. Ramos; Pedro A. Fernandes. "Unraveling the Reaction Mechanism
of Russell’s Viper Venom Factor X Activator: A Paradigm for the Reactivity of Zinc Metalloproteinases?". Journal of Chemical
Information and Modeling (2023): https://doi.org/10.1021/acs.jcim.2c01156.
10.1021/acs.jcim.2c01156
- João Sousa; Nuno Azevedo Oliveira; Pedro Alexandrino Fernandes. "Rational Engineering of (S)-Norcoclaurine Synthase
for Efficient Benzylisoquinoline Alkaloids Biosynthesis". Molecules (2023): https://www.mdpi.com/1420-3049/28/11/4265.
10.3390/molecules28114265
- Juliana Castro-Amorim; Ana Novo de Oliveira; Saulo Luís Da Silva; Andreimar M. Soares; Ashis K. Mukherjee; Maria João Ramos;
Pedro A. Fernandes. "Catalytically Active Snake Venom PLA2 Enzymes: An Overview of Its Elusive Mechanisms of Reaction". Journal
of Medicinal Chemistry (2023): https://doi.org/10.1021/acs.jmedchem.3c00097.
10.1021/acs.jmedchem.3c00097
- Rui P. P. Neves; Bruno Araújo; Maria J. Ramos; Pedro A. Fernandes. "Feedback Inhibition of DszC, a Crucial Enzyme for Crude
Oil Biodessulfurization". Catalysts (2023): https://doi.org/10.3390/catal13040736.
10.3390/catal13040736
- Carlos F. M. Silva; Teresa Leão; Filipa Dias; Ana M. Tomás; Diana C. G. A. Pinto; Eduardo F. T. Oliveira; Ana Oliveira; Pedro
A. Fernandes; Artur M. S. Silva. "Structure–Activity Relationship Studies of 9-Alkylamino-1,2,3,4-tetrahydroacridines against
Leishmania (Leishmania) infantum Promastigotes". Pharmaceutics (2023): https://doi.org/10.3390/pharmaceutics15020669.
10.3390/pharmaceutics15020669
- Alexandre V. Pinto; Pedro Ferreira; Pedro A. Fernandes; Alexandre L. Magalhães; Maria J. Ramos. "Development of Nanoscale
Graphene Oxide Models for the Adsorption of Biological Molecules". The Journal of Physical Chemistry B (2023): https://doi.org/10.1021/acs.jpcb.2c06037.
10.1021/acs.jpcb.2c06037
- Rui P. P. Neves; Maria J. Ramos; Pedro A. Fernandes. "Engineering DszC Mutants from Transition State Macrodipole Considerations
and Evolutionary Sequence Analysis". Journal of Chemical Information and Modeling (2023): https://doi.org/10.1021/acs.jcim.2c01337.
10.1021/acs.jcim.2c01337
- Ong, How Chee; Coimbra, João T. S.; Ramos, Maria Joao Joao; Xing, Bengang; Fernandes, Pedro Alexandrino; García, Felipe. "Beyond
the TPP+ “gold standard”: A new generation mitochondrial delivery vector based on extended PN frameworks.". Chemical Science
(2023): http://dx.doi.org/10.1039/d2sc06508h.
10.1039/d2sc06508h
- How Chee Ong; João T. S. Coimbra; Maria J. Ramos; Bengang Xing; Pedro A. Fernandes; Felipe García. "Beyond the TPP+ “gold
standard”: a new generation mitochondrial delivery vector based on extended PN frameworks". Chemical Science (2023):
https://doi.org/10.1039/D2SC06508H.
10.1039/D2SC06508H
- Matilde F. Viegas; Rui P. P. Neves; Maria J. Ramos; Pedro A. Fernandes. "QM/MM Study of the Reaction Mechanism of Thermophilic
Glucuronoyl Esterase for Biomass Treatment". ChemPhysChem (2022): https://doi.org/10.1002/cphc.202200269.
10.1002/cphc.202200269
- Rui P. P. Neves; Pedro A. Fernandes; Maria J. Ramos. "Role of Enzyme and Active Site Conformational Dynamics in the Catalysis
by a-Amylase Explored with QM/MM Molecular Dynamics". Journal of Chemical Information and Modeling (2022): https://doi.org/10.1021/acs.jcim.2c00691.
10.1021/acs.jcim.2c00691
- João T. S. Coimbra; Rui P. P. Neves; Ana V. Cunha; Maria J. Ramos; Pedro A. Fernandes. "Cover Feature: Different Enzyme Conformations
Induce Different Mechanistic Traits in HIV-1 Protease (Chem. Eur. J. 42/2022)". Chemistry – A European Journal (2022):
https://doi.org/10.1002/chem.202202001.
10.1002/chem.202202001
- João T. S. Coimbra; Rui P. P. Neves; Ana V. Cunha; Maria J. Ramos; Pedro A. Fernandes. "Different Enzyme Conformations Induce
Different Mechanistic Traits in HIV-1 Protease". Chemistry – A European Journal (2022): https://doi.org/10.1002/chem.202201066.
10.1002/chem.202201066
- Rui P. P. Neves; Ana V. Cunha; Pedro A. Fernandes; Maria J. Ramos. "Towards the Accurate Thermodynamic Characterization of
Enzyme Reaction Mechanisms". ChemPhysChem 23 13 (2022): https://doi.org/10.1002/cphc.202200159.
10.1002/cphc.202200159
- Ana L. Oliveira; Matilde F. Viegas; Saulo L. da Silva; Andreimar M. Soares; Maria J. Ramos; Pedro A. Fernandes. "The chemistry
of snake venom and its medicinal potential". Nature Reviews Chemistry (2022): https://doi.org/10.1038/s41570-022-00393-7.
10.1038/s41570-022-00393-7
- Luís M. C. Teixeira; João T. S. Coimbra; Maria João Ramos; Pedro Alexandrino Fernandes. "Transmembrane Protease Serine 2 Proteolytic
Cleavage of the SARS-CoV-2 Spike Protein: A Mechanistic Quantum Mechanics/Molecular Mechanics Study to Inspire the Design
of New Drugs To Fight the COVID-19 Pandemic". Journal of Chemical Information and Modeling (2022): https://doi.org/10.1021/acs.jcim.1c01561.
10.1021/acs.jcim.1c01561
- Pedro A. Fernandes; Óscar Passos; Maria J. Ramos. "Necessity is the Mother of Invention: A Remote Molecular Bioinformatics
Practical Course in the COVID-19 Era". Journal of Chemical Education (2022): https://doi.org/10.1021/acs.jchemed.1c01195.
10.1021/acs.jchemed.1c01195
- "Exploring the permeation of fluoroquinolone metalloantibiotics across outer membrane porins by combining molecular dynamics
simulations and a porin-mimetic in vitro model". Biochimica et Biophysica Acta (BBA) - Biomembranes 1864 3 (2022):
183838-183838. http://dx.doi.org/10.1016/j.bbamem.2021.183838.
10.1016/j.bbamem.2021.183838
- "The archaeal non-heme iron-containing Sulfur Oxygenase Reductase". Coordination Chemistry Reviews 455 (2022): 214358-214358.
http://dx.doi.org/10.1016/j.ccr.2021.214358.
10.1016/j.ccr.2021.214358
- "Engineering of PKS Megaenzymes—A Promising Way to Biosynthesize High-Value Active Molecules". Topics in Catalysis
65 1-4 (2022): 544-562. http://dx.doi.org/10.1007/s11244-021-01490-5.
10.1007/s11244-021-01490-5
- Carlos F. M. Silva; Diana C. G. A. Pinto; Pedro A. Fernandes; Artur M. S. Silva. "Evolution of Acridines and Xanthenes as
a Core Structure for the Development of Antileishmanial Agents". Pharmaceuticals (2022): https://doi.org/10.3390/ph15020148.
10.3390/ph15020148
- João P. M. Sousa; Maria J. Ramos; Pedro A. Fernandes. "Modern Strategies for the Diversification of the Supply of Natural
Compounds: The Case of Alkaloid Painkillers". ChemBioChem (2022): https://doi.org/10.1002/cbic.202100623.
10.1002/cbic.202100623
- Carina Proença; Ana T. Rufino; José Miguel P. Ferreira de Oliveira; Marisa Freitas; Pedro A. Fernandes; Artur M. S. Silva;
Eduarda Fernandes. "Inhibitory activity of flavonoids against human sucrase-isomaltase (a-glucosidase) activity in a Caco-2/TC7
cellular model". Food & Function (2022): https://doi.org/10.1039/D1FO02995A.
10.1039/D1FO02995A
- Anna Cebrián-Prats; Alexandre Pinto; Àngels González-Lafont; Pedro A. Fernandes; José M. Lluch. "The role of acetylated cyclooxygenase-2
in the biosynthesis of resolvin precursors derived from eicosapentaenoic acid". Organic & Biomolecular Chemistry (2022):
https://doi.org/10.1039/D1OB01932E.
10.1039/D1OB01932E
- Ferreira, P; Fernandes, PA; Ramos, MJ. "Modern computational methods for rational enzyme engineering". CHEM CATALYSIS
(2022): https://www.authenticus.pt/P-00X-D5M.
10.1016/j.checat.2022.09.036
- Amaral, LMPF; Moniz, T; Leite, A; Oliveira, A; Fernandes, P; Ramos, MJ; Araujo, AN; et al. "A combined experimental and computational
study to discover novel tyrosinase inhibitors". JOURNAL OF INORGANIC BIOCHEMISTRY (2022): https://www.authenticus.pt/P-00W-PVQ.
10.1016/j.jinorgbio.2022.111879
- Perrin, CL; Agranat, I; Bagno, A; Braslavsky, SE; Fernandes, PA; Gal, JF; Lloyd-Jones, GC; et al. "Glossary of terms used
in physical organic chemistry (IUPAC Recommendations 2021)". PURE AND APPLIED CHEMISTRY (2022): https://www.authenticus.pt/P-00W-QNK.
10.1515/pac-2018-1010
- João Marques Sousa; Matilde Ribeiro Viegas; Pedro Teixeira Ferreira; Pedro Coelho Paiva; Ana Luísa Oliveira; Pedro Alexandrino
Fernandes; Maria João Ramos. "MOLECULAR BIOINFORMATICS". Revista de Ciência Elementar 9 4 (2021): https://doi.org/10.24927/rce2021.075.
10.24927/rce2021.075
- Pedro Fernandes; Francisco Félix. "“Tão natural”". Revista de Ciência Elementar (2021): https://doi.org/10.24927/rce2021.072.
10.24927/rce2021.072
- "Lessons from a Single Amino Acid Substitution: Anticancer and Antibacterial Properties of Two Phospholipase A2-Derived Peptides".
Current Issues in Molecular Biology 44 1 (2021): 46-62. http://dx.doi.org/10.3390/cimb44010004.
10.3390/cimb44010004
- Upasana Puzari; Pedro Alexandrino Fernandes; Ashis K. Mukherjee. "Advances in the Therapeutic Application of Small-Molecule
Inhibitors and Repurposed Drugs against Snakebite". Journal of Medicinal Chemistry 64 19 (2021): 13938-13979. https://doi.org/10.1021/acs.jmedchem.1c00266.
10.1021/acs.jmedchem.1c00266
- "The Catalytic Mechanism of the Retaining Glycosyltransferase Mannosylglycerate Synthase". Chemistry – A European Journal
27 56 (2021): 13998-14006. http://dx.doi.org/10.1002/chem.202101724.
10.1002/chem.202101724
- Carola Jerves; Rui P. P. Neves; Maria J. Ramos; Saulo da Silva; Pedro A. Fernandes. "Reaction Mechanism of the PET Degrading
Enzyme PETase Studied with DFT/MM Molecular Dynamics Simulations". ACS Catalysis (2021): https://doi.org/10.1021/acscatal.1c03700.
10.1021/acscatal.1c03700
- Alexandre V. Pinto; Pedro Ferreira; Rui P. P. Neves; Pedro A. Fernandes; Maria J. Ramos; Alexandre L. Magalhães. "Reaction
Mechanism of MHETase, a PET Degrading Enzyme". ACS Catalysis (2021): 10416-10428. https://doi.org/10.1021/acscatal.1c02444.
10.1021/acscatal.1c02444
- Pedro Paiva; Fabiola E. Medina; Matilde Viegas; Pedro Ferreira; Rui P. P. Neves; João P. M. Sousa; Maria J. Ramos; Pedro A.
Fernandes. "Animal Fatty Acid Synthase: A Chemical Nanofactory". Chemical Reviews (2021): https://doi.org/10.1021/acs.chemrev.1c00147.
10.1021/acs.chemrev.1c00147
- Matilde Viegas; Maria João Ramos; Pedro Alexandrino Fernandes. "Thermophilic Enzymes". U.Porto Journal of Engineering
(2021): https://doi.org/10.24840/2183-6493_007.003_0002.
10.24840/2183-6493_007.003_0002
- "Chromeno[3,4-b]xanthones as First-in-Class AChE and Aß Aggregation Dual-Inhibitors". International Journal of Molecular
Sciences 22 8 (2021): 4145-4145. http://dx.doi.org/10.3390/ijms22084145.
10.3390/ijms22084145
- "Passive Diffusion of Ciprofloxacin and its Metalloantibiotic: A Computational and Experimental study". Journal of Molecular
Biology 433 9 (2021): 166911-166911. http://dx.doi.org/10.1016/j.jmb.2021.166911.
10.1016/j.jmb.2021.166911
- João T. S. Coimbra; Ralph Feghali; Rui P. Ribeiro; Maria J. Ramos; Pedro A. Fernandes; Coimbra, J.T.S.; Feghali, R.; et al.
"The importance of intramolecular hydrogen bonds on the translocation of the small drug piracetam through a lipid bilayer".
RSC Advances 11 2 (2021): 899-908. https://doi.org/10.1039/D0RA09995C.
10.1039/D0RA09995C
- Almeida, C.F.; Teixeira, N.; Oliveira, A.; Augusto, T.V.; Correia-da-Silva, G.; Ramos, M.J.; Fernandes, P.A.; Amaral, C..
"Discovery of a multi-target compound for estrogen receptor-positive (ER+) breast cancer: Involvement of aromatase
and ERs". Biochimie 181 (2021): 65-76. http://www.scopus.com/inward/record.url?eid=2-s2.0-85097475676&partnerID=MN8TOARS.
10.1016/j.biochi.2020.11.023
- Resende, L.M.; Almeida, J.R.; Guaraca-Medina, T.A.; Viegas, M.F.; Soares, A.M.; Ramos, M.J.; Fernandes, P.A.; Marangoni, S.;
Da Silva, S.L.. "Structural, enzymatic and pharmacological profiles of AplTX-II - A basic sPLA2 (D49) isolated
from the Agkistrodon piscivorus leucostoma snake venom". International Journal of Biological Macromolecules 175 (2021):
572-585. http://www.scopus.com/inward/record.url?eid=2-s2.0-85100730003&partnerID=MN8TOARS.
10.1016/j.ijbiomac.2021.01.187
- Brás, N.F.; Ferreira, P.; Calixto, A.R.; Jaspars, M.; Houssen, W.; Naismith, J.H.; Fernandes, P.A.; Ramos, M.J.. "Corrigendum:
The Catalytic Mechanism of the Marine-Derived Macrocyclase PatGmac (Chemistry - A European Journal, (2016), 22, 37, (13089-13097),
10.1002/chem.201601670)". Chemistry - A European Journal (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85099750694&partnerID=MN8TOARS.
10.1002/chem.202100062
- Jordi Soler; Pedro Paiva; Maria J. Ramos; Pedro A. Fernandes; Marie Brut. "Unraveling the cGAS catalytic mechanism upon DNA
activation through molecular dynamics simulations". Physical Chemistry Chemical Physics (2021): https://doi.org/10.1039/D1CP00378J.
10.1039/D1CP00378J
- How Chee Ong; João T. S. Coimbra; Germain Kwek; Maria J. Ramos; Bengang Xing; Pedro A. Fernandes; Felipe García. "Alkyl vs.
aryl modifications: a comparative study on modular modifications of triphenylphosphonium mitochondrial vectors". RSC Chemical
Biology (2021): https://doi.org/10.1039/D1CB00099C.
10.1039/D1CB00099C
- Carlos F. M. Silva; Diana C. G. A. Pinto; Pedro A. Fernandes; Artur M. S. Silva. "Evolution of chromone-like compounds as
potential antileishmanial agents, through the 21st century". Expert Opinion on Drug Discovery (2020): 1-15. https://doi.org/10.1080/17460441.2020.1801630.
10.1080/17460441.2020.1801630
- Kenneth Goossens; Rui PP Neves; Pedro A Fernandes; Hans De Winter. "A Computational and Modeling Study of the Reaction Mechanism
of Staphylococcus aureus Monoglycosyltransferase Reveals New Insights on the GT51 Family of Enzymes". Journal of Chemical
Information and Modeling (2020): https://doi.org/10.1021/acs.jcim.0c00377.
10.1021/acs.jcim.0c00377
- Pedro Paiva; Maria J. Ramos; Pedro A. Fernandes. "Assessing the validity of DLPNO-CCSD (T) in the calculation of activation
and reaction energies of ubiquitous enzymatic reactions". Journal of Computational Chemistry (2020): https://doi.org/10.1002/jcc.26401.
10.1002/jcc.26401
- Pedro Ferreira; Nuno M. F. Sousa A. Cerqueira; Pedro Alexandrino Fernandes; Maria João Romão; Maria João Ramos. "Catalytic
Mechanism of Human Aldehyde Oxidase". ACS Catalysis (2020): 9276-9286. https://doi.org/10.1021/acscatal.0c02627.
10.1021/acscatal.0c02627
- João P. M. Sousa; Rui P. P. Neves; Sérgio F. Sousa; Maria J. Ramos; Pedro A. Fernandes. "Reaction Mechanism and Determinants
for Efficient Catalysis by DszB, a Key Enzyme for Crude Oil Bio-desulfurization". ACS Catalysis (2020): 9545-9554.
https://doi.org/10.1021/acscatal.0c03122.
10.1021/acscatal.0c03122
- Fernandes, Pedro Alexandrino. "Activation free energy, substrate binding free energy and enzyme efficiency fall in a very
narrow range of values for most enzymes". ACS Catalysis (2020): https://pubs.acs.org/doi/10.1021/acscatal.0c01947.
10.1021/acscatal.0c01947
- Pedro Fernandes; Maria João Ramos. "O sabão contra a COVID-19". Revista de Ciência Elementar 8 2 (2020): https://doi.org/10.24927/rce2020.019.
10.24927/rce2020.019
- Pedro Fernandes; Maria João Ramos. "O álcool contra a COVID-19". Revista de Ciência Elementar 8 2 (2020): https://doi.org/10.24927/rce2020.018.
10.24927/rce2020.018
- Pedro Fernandes. "A Ciência é a única arma". Revista de Ciência Elementar (2020): https://doi.org/10.24927/rce2020.017.
10.24927/rce2020.017
- Carina Proença; Ana Oliveira; Marisa Freitas; Daniela Ribeiro; Joana L. C. Sousa; Maria J. Ramos; Artur M. S. Silva; Pedro
A. Fernandes; Eduarda Fernandes. "Structural Specificity of Flavonoids in the Inhibition of Human Fructose 1,6-Bisphosphatase".
Journal of Natural Products (2020): https://doi.org/10.1021/acs.jnatprod.0c00014.
10.1021/acs.jnatprod.0c00014
- Mario Prejano; Fabiola E. Medina; Maria J. Ramos; Nino Russo; Pedro A. Fernandes; Tiziana Marino. "Correction to “How the
Destabilization of a Reaction Intermediate Affects Enzymatic Efficiency: The Case of Human Transketolase”". ACS Catalysis
(2020): 5372-5372. https://doi.org/10.1021/acscatal.0c01697.
10.1021/acscatal.0c01697
- Fernandes, Pedro Alexandrino. "Cannabidiol (CBD) but not tetrahydrocannabinol (THC) dysregulate in vitro decidualization of
human endometrial stromal cells by disruption of estrogen signaling". Reproductive Toxicology (2020): http://dx.doi.org/10.1016/j.reprotox.2020.01.003.
10.1016/j.reprotox.2020.01.003
- Mario Prejanò; Fabiola E. Medina; Maria J. Ramos; Nino Russo; Pedro A. Fernandes; Tiziana Marino. "How the Destabilization
of a Reaction Intermediate Affects Enzymatic Efficiency: The Case of Human Transketolase". ACS Catalysis (2020): https://doi.org/10.1021/acscatal.9b04690.
10.1021/acscatal.9b04690
- Sousa, R.; Moorthy, N.S.H.N.; Fernandes, P.A.; Ramos, M.J.; Brás, N.F.. "Binding mode prediction and identification of new
lead compounds from natural products as 3-OST enzyme inhibitors". Letters in Drug Design and Discovery 17 9 (2020):
1186-1196. http://www.scopus.com/inward/record.url?eid=2-s2.0-85090677162&partnerID=MN8TOARS.
10.2174/1570180817666200313105944
- Ferreira Almeida, C.; Oliveira, A.; João Ramos, M.; Fernandes, P.A.; Teixeira, N.; Amaral, C.. "Estrogen receptor-positive
(ER+) breast cancer treatment: Are multi-target compounds the next promising approach?". Biochemical Pharmacology
177 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85084205378&partnerID=MN8TOARS.
10.1016/j.bcp.2020.113989
- Sousa, J.P.M.; Ferreira, P.; Neves, R.P.P.; Ramos, M.J.; Fernandes, P.A.. "The bacterial 4S pathway-an economical alternative
for crude oil desulphurization that r educes CO2emissions". Green Chemistry 22 22 (2020): 7604-7621. http://www.scopus.com/inward/record.url?eid=2-s2.0-85096760072&partnerID=MN8TOARS.
10.1039/d0gc02055a
- Pedro Fernandes. "Fraudes e falsificações na Arte e Arqueologia desmascaradas pela datação por Carbono 14". Revista de
Ciência Elementar 7 4 (2019): https://doi.org/10.24927/rce2019.072.
10.24927/rce2019.072
- Fernandes, Pedro. "The Catalytic Mechanism of Human Transketolase". ChemPhysChem (2019): http://dx.doi.org/10.1002/cphc.201900650.
10.1002/cphc.201900650
- Fernandes, Pedro. "Human Fatty Acid Synthase: A Computational Study of the Transfer of the Acyl Moieties from MAT to the ACP
Domain". ChemCatChem (2019): http://dx.doi.org/10.1002/cctc.201900548.
10.1002/cctc.201900548
- Fernandes, Pedro. "Anandamide targets aromatase: A breakthrough on human decidualization". Biochimica et Biophysica Acta
(BBA) - Molecular and Cell Biology of Lipids (2019): http://dx.doi.org/10.1016/j.bbalip.2019.08.008.
10.1016/j.bbalip.2019.08.008
- Fernandes, Pedro. "Glutamine synthetase structure-catalysis relationship—Recent advances and applications". Wiley Interdisciplinary
Reviews: Computational Molecular Science (2019): http://dx.doi.org/10.1002/wcms.1399.
10.1002/wcms.1399
- Fernandes, Pedro. "Enabling Mitochondrial Uptake of Lipophilic Dications Using Methylated Triphenylphosphonium Moieties".
Inorganic Chemistry (2019): http://dx.doi.org/10.1021/acs.inorgchem.8b03380.
10.1021/acs.inorgchem.8b03380
- Fernandes, Pedro. "Benchmark of Density Functionals for the Calculation of the Redox Potential of Fe3+/Fe2+ Within Protein
Coordination Shells". Frontiers in Chemistry (2019): http://dx.doi.org/10.3389/fchem.2019.00391.
10.3389/fchem.2019.00391
- Fernandes, Pedro. "A computational study on the redox properties and binding affinities of iron complexes of hydroxypyridinones".
Journal of Molecular Modeling (2019): http://dx.doi.org/10.1007/s00894-019-4037-0.
10.1007/s00894-019-4037-0
- Fernandes, Pedro. "Structural and mechanistic aspects of S-S bonds in the thioredoxin-like family of proteins". Biological
Chemistry (2019): http://dx.doi.org/10.1515/hsz-2018-0319.
10.1515/hsz-2018-0319
- Carina Proença; Marisa Freitas; Daniela Ribeiro; Sara M. Tomé; Eduardo F. T. Oliveira; Matilde F. Viegas; Alberto N. Araújo;
et al. "Evaluation of a flavonoids library for inhibition of pancreatic a-amylase towards a structure–activity relationship".
Journal of Enzyme Inhibition and Medicinal Chemistry (2019): https://doi.org/10.1080/14756366.2018.1558221.
10.1080/14756366.2018.1558221
- Wilson, K. A.; Fernandes, P. A.; Ramos, M. J.; Wetmore, S. D.. "Exploring the Identity of the General Base for a DNA Polymerase
Catalyzed Reaction Using QM/MM: The Case Study of Human Translesion Synthesis Polymerase eta". Acs Catalysis 9 3 (2019):
2543-2551. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000460600600086&KeyUID=WOS:000460600600086.
10.1021/acscatal.8b04889
- Gameiro, P.; Sousa, C. F.; Coimbra, J. T. S.; Fernandes, P. A.; Ramos, M. J.. "Drug Permeation Across the Bacterial Membrane:
Combining Theoretical and Experimental Approaches". Biophysical Journal 116 3 (2019): 206A-206A. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000460779801038&KeyUID=WOS:000460779801038.
10.1016/j.bpj.2018.11.1138
- Ana Rita Calixto; Maria João Ramos; Pedro Alexandrino Fernandes; Calixto, A.R.; Ramos, M.J.; Fernandes, P.A.. "Conformational
diversity induces nanosecond-timescale chemical disorder in the HIV-1 protease reaction pathway". Chemical Science
10 30 (2019): 7212-7221. https://doi.org/10.1039/C9SC01464K.
10.1039/C9SC01464K
- Carina Proença; Marisa Freitas; Daniela Ribeiro; Sara M. Tomé; Alberto N. Araújo; Artur M. S. Silva; Pedro A. Fernandes; et
al. "The dipeptidyl peptidase-4 inhibitory effect of flavonoids is hindered in protein rich environments". Food & Function
10 9 (2019): 5718-5731. https://doi.org/10.1039/C9FO00722A.
10.1039/C9FO00722A
- Medina, F.E.; Ramos, M.J.; Fernandes, P.A.. "Complexities of the Reaction Mechanisms of CC Double Bond Reduction in Mammalian
Fatty Acid Synthase Studied with Quantum Mechanics/Molecular Mechanics Calculations". ACS Catalysis 9 12 (2019): 11404-11412.
http://www.scopus.com/inward/record.url?eid=2-s2.0-85075061675&partnerID=MN8TOARS.
10.1021/acscatal.9b03531
- Ferreira, P.; Cerqueira, N.M.F.S.A.; Coelho, C.; Fernandes, P.A.; Romão, M.J.; Ramos, M.J.; P. Ferreira; et al. "New insights
about the monomer and homodimer structures of the human AOX1". Physical Chemistry Chemical Physics 21 25 (2019): 13545-13554.
http://www.scopus.com/inward/record.url?eid=2-s2.0-85068418264&partnerID=MN8TOARS.
10.1039/c9cp01040h
- Matilde Viegas; Maria João Ramos; Pedro Fernandes. "Biocombustíveis, serão a solução?". Revista de Ciência Elementar
(2018): https://doi.org/10.24927/rce2018.043.
10.24927/rce2018.043
- Bras, N. F.; Fernandes, P. A.; Ramos, M. J.; Schwartz, S. D.. "Mechanistic Insights on Human Phosphoglucomutase Revealed by
Transition Path Sampling and Molecular Dynamics Calculations". Chemistry-a European Journal 24 8 (2018): 1978-1987.
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000424226000031&KeyUID=WOS:000424226000031.
10.1002/chem.201705090
- Proenca, C.; Freitas, M.; Ribeiro, D.; Sousa, J. L. C.; Carvalho, F.; Silva, A. M. S.; Fernandes, P. A.; Fernandes, E.. "Inhibition
of protein tyrosine phosphatase 1B by flavonoids: A structure activity relationship study". Food and Chemical Toxicology
111 (2018): 474-481. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000423248100042&KeyUID=WOS:000423248100042.
10.1016/j.fct.2017.11.039
- Jana, G. A.; Mendoza, F.; Osorio, M. I.; Alderete, J. B.; Fernandes, P. A.; Ramos, M. J.; Jimenez, V. A.. "A QM/MM approach
on the structural and stereoelectronic factors governing glycosylation by GTF-SI from Streptococcus mutans". Organic &
Biomolecular Chemistry 16 14 (2018): 2438-2447. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000429204000010&KeyUID=WOS:000429204000010.
10.1039/c8ob00284c
- Almeida, J. R.; Mendes, B.; Lancellotti, M.; Marangoni, S.; Vale, N.; Passos, O.; Ramos, M. J.; et al. "A novel synthetic
peptide inspired on Lys49 phospholipase A(2) from Crotalus oreganus abyssus snake venom active against multidrug-resistant
clinical isolates". European Journal of Medicinal Chemistry 149 (2018): 248-256. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000429186900022&KeyUID=WOS:000429186900022.
10.1016/j.ejmech.2018.02.055
- Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "Visualizing the Microscopic World". Interdisciplinary Sciences-Computational
Life Sciences 10 1 (2018): 105-110. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000426823400010&KeyUID=WOS:000426823400010.
10.1007/s12539-017-0255-2
- Paiva, P.; Costa, I. P. D.; Ferreira, C. E.; Ferreira, P.; Pereira, A. T.; Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J..
"Studies on neuraminidase inhibition". International Journal of Quantum Chemistry 118 9 (2018): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000428413300014&KeyUID=WOS:000428413300014.
10.1002/qua.25592
- Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "Protocol for Computational Enzymatic Reactivity Based on Geometry Optimisation".
Chemphyschem 19 6 (2018): 669-689. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000428380500001&KeyUID=WOS:000428380500001.
10.1002/cphc.201700339
- Ferreira, P.; Cerqueira, Nmfsa; Bras, N. F.; Fernandes, P. A.; Ramos, M. J.. "Parametrization of Molybdenum Cofactors for
the AMBER Force Field". Journal of Chemical Theory and Computation 14 5 (2018): 2538-2548. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000431926500023&KeyUID=WOS:000431926500023.
10.1021/acs.jctc.8b00137
- Viegas, M. F.; Neves, R. P. P.; Ramos, M. J.; Fernandes, P. A.. "Modeling of Human Fatty Acid Synthase and &ITin Silico&IT
Docking of Acyl Carrier Protein Domain and Its Partner Catalytic Domains". Journal of Physical Chemistry B 122 1 (2018):
77-85. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000422814000008&KeyUID=WOS:000422814000008.
10.1021/acs.jpcb.7b09645
- Bras, N. F.; Santos-Martins, D.; Fernandes, P. A.; Ramos, M. J.. "Mechanistic Pathway on Human alpha-Glucosidase Maltase-Glucoamylase
Unveiled by QM/MM Calculations". Journal of Physical Chemistry B 122 14 (2018): 3889-3899. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000430641900020&KeyUID=WOS:000430641900020.
10.1021/acs.jpcb.8b01321
- Friedman, R.; Khalid, S.; Aponte-Santamaria, C.; Arutyunova, E.; Becker, M.; Boyd, K. J.; Christensen, M.; et al. "Understanding
Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology". Journal of Membrane Biology 251 5-6 (2018):
609-631. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000450567200001&KeyUID=WOS:000450567200001.
10.1007/s00232-018-0050-y
- Bras, N. F.; Fernandes, P. A.; Ramos, M. J.. "Understanding the Rate-Limiting Step of Glycogenolysis by Using QM/MM Calculations
on Human Glycogen Phosphorylase". Chemmedchem 13 15 (2018): 1608-1616. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000441432700013&KeyUID=WOS:000441432700013.
10.1002/cmdc.201800218
- Santos-Martins, D.; Calixto, A. R.; Fernandes, P. A.; Ramos, M. J.. "A Buried Water Molecule Influences Reactivity in a alpha-Amylase
on a Subnanosecond Time Scale". Acs Catalysis 8 5 (2018): 4055-4063. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000431727300039&KeyUID=WOS:000431727300039.
10.1021/acscatal.7b04400
- Paiva, P.; Sousa, S. F.; Ramos, M. J.; Fernandes, P. A.. "Understanding the Catalytic Machinery and the Reaction Pathway of
the Malonyl-Acetyl Transferase Domain of Human Fatty Acid Synthase". Acs Catalysis 8 6 (2018): 4860-4872. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000434369600014&KeyUID=WOS:000434369600014.
10.1021/acscatal.8b00577
- Silva, A. M. N.; Coimbra, J. T. S.; Castro, M. M.; Oliveira, A.; Bras, N. F.; Fernandes, P. A.; Ramos, M. J.; Rangel, M..
"Determining the glycation site specificity of human holo-transferrin". Journal of Inorganic Biochemistry 186 (2018):
95-102. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000441704600012&KeyUID=WOS:000441704600012.
10.1016/j.jinorgbio.2018.05.016
- Coimbra, J. T. S.; Bras, N. F.; Fernandes, P. A.; Rangel, M.; Ramos, M. J.. "Membrane partition of bis-(3-hydroxy-4pyridinonato)
zinc(ii) complexes revealed by molecular dynamics simulations". Rsc Advances 8 48 (2018): 27081-27090. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000445747800010&KeyUID=WOS:000445747800010.
10.1039/c8ra03602k
- Barbosa, A. C. C.; Neves, R. P. P.; Sousa, S. F.; Ramos, M. J.; Fernandes, P. A.. "Mechanistic Studies of a Flavin Monooxygenase:
Sulfur Oxidation of Dibenzothiophenes by DszC". Acs Catalysis 8 10 (2018): 9298-9311. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000447224100036&KeyUID=WOS:000447224100036.
10.1021/acscatal.8b01877
- Simoes, I. C. M.; Coimbra, J. T. S.; Neves, R. P. P.; Costa, I. P. D.; Ramos, M. J.; Fernandes, P. A.; Inês C. M. Simões;
et al. "Properties that rank protein: protein docking poses with high accuracy". Physical Chemistry Chemical Physics
20 32 (2018): 20927-20942. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000447367900018&KeyUID=WOS:000447367900018.
10.1039/c8cp03888k
- Ramos, M. J.; Fernandes, P. A.. "Structure, Dynamics, and Energetics of ATP Hydrolysis by ABC Transporters". Acs Central
Science 4 10 (2018): 1300-1302. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000448053200005&KeyUID=WOS:000448053200005.
10.1021/acscentsci.8b00631
- Medina, F. E.; Neves, R. P. P.; Ramos, M. J.; Fernandes, P. A.; Medina, F.E.; Neves, R.P.P.; Ramos, M.J.; Fernandes, P.A..
"QM/MM Study of the Reaction Mechanism of the Dehydratase Domain from Mammalian Fatty Acid Synthase". Acs Catalysis
8 11 (2018): 10267-10278. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000449723900039&KeyUID=WOS:000449723900039.
10.1021/acscatal.8602616
- Pedro Fernandes; Ana Calixto. "Moléculas magníficas". Revista de Ciência Elementar 5 2 (2017): https://doi.org/10.24927%2Frce2017.027.
10.24927/rce2017.027
- Calixto, A. R.; Ramos, M. J.; Fernandes, P. A.. "Influence of Frozen Residues on the Exploration of the PES of Enzyme Reaction
Mechanisms". Journal of Chemical Theory and Computation 13 11 (2017): 5486-5495. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000415911800027&KeyUID=WOS:000415911800027.
10.1021/acs.jctc.7b00768
- Ferreira, P.; Sousa, S. F.; Fernandes, P. A.; Ramos, M. J.. "Improving the Catalytic Power of the DszD Enzyme for the Biodesulfurization
of Crude Oil and Derivatives". Chemistry-a European Journal 23 68 (2017): 17231-17241. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000419670200001&KeyUID=WOS:000419670200001.
10.1002/chem.201704057
- Sousa, C. F.; Coimbra, J. T. S.; Ferreira, M.; Ramos, M. J.; Fernandes, P. A.; Gameiro, P.. "Exploring the permeation of free
and copper-complexed fluoroquinolones across the bacterial membrane". European Biophysics Journal with Biophysics Letters
46 (2017): S269-S269. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000416406201481&KeyUID=WOS:000416406201481.
- Ribeiro, R. P.; Coimbra, J. T. S.; Ramos, M. J.; Fernandes, P. A.. "Diffusion of the small, very polar, drug piracetam through
a lipid bilayer: an MD simulation study". Theoretical Chemistry Accounts 136 4 (2017): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000404246000001&KeyUID=WOS:000404246000001.
10.1007/s00214-017-2073-3
- Moreira, C.; Ramos, M. J.; Fernandes, P. A.. "Clarifying the Catalytic Mechanism of Human Glutamine Synthetase: A QM/MM Study".
Journal of Physical Chemistry B 121 26 (2017): 6313-6320. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000405253000004&KeyUID=WOS:000405253000004.
10.1021/acs.jpcb.7b02543
- Barra, P. A.; Ribeiro, A. J. M.; Ramos, M. J.; Jimenez, V. A.; Alderete, J. B.; Fernandes, P. A.. "Binding free energy calculations
on E-selectin complexes with sLe(x) oligosaccharide analogs". Chemical Biology & Drug Design 89 1 (2017): 114-123.
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000390354100010&KeyUID=WOS:000390354100010.
10.1111/cbdd.12837
- Pereira, A. T.; Ribeiro, A. J. M.; Fernandes, P. A.; Ramos, M. J.. "Benchmarking of density functionals for the kinetics and
thermodynamics of the hydrolysis of glycosidic bonds catalyzed by glycosidases". International Journal of Quantum Chemistry
117 18 (2017): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000406687800002&KeyUID=WOS:000406687800002.
10.1002/qua.25409
- Sousa, S. F.; Ribeiro, A. J. M.; Neves, R. P. P.; Bras, N. F.; Cerqueira, Nmfsa; Fernandes, P. A.; Ramos, M. J.. "Application
of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms". Wiley Interdisciplinary
Reviews-Computational Molecular Science 7 2 (2017): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000399013100004&KeyUID=WOS:000399013100004.
10.1002/wcms.1281
- Hu, Z.; Sim, Y.; Kon, O. L.; Ng, W. H.; Ribeiro, A. J. M.; Ramos, M. J.; Fernandes, P. A.; et al. "Unique Triphenylphosphonium
Derivatives for Enhanced Mitochondrial Uptake and Photodynamic Therapy". Bioconjugate Chemistry 28 2 (2017): 590-599.
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000394481700036&KeyUID=WOS:000394481700036.
10.1021/acs.bioconjchem.6b00682
- Cerqueira, Nmfsa; Moorthy, H.; Fernandes, P. A.; Ramos, M. J.. "The mechanism of the Ser-(cis)Ser-Lys catalytic triad of peptide
amidases". Physical Chemistry Chemical Physics 19 19 (2017): 12343-12354. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000401640600062&KeyUID=WOS:000401640600062.
10.1039/c7cp00277g
- Coimbra, J. T. S.; Fernandes, P. A.; Ramos, M. J.. "Revisiting Partition in Hydrated Bilayer Systems". Journal of Chemical
Theory and Computation 13 5 (2017): 2290-2299. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000401221300036&KeyUID=WOS:000401221300036.
10.1021/acs.jctc.6b01258
- Simoes, I. C. M.; Costa, I. P. D.; Coimbra, J. T. S.; Ramos, M. J.; Fernandes, P. A.. "New Parameters for Higher Accuracy
in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein-Protein Interfaces". Journal
of Chemical Information and Modeling 57 1 (2017): 60-72. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000392687400008&KeyUID=WOS:000392687400008.
10.1021/acs.jcim.6b00378
- Merski, M.; Moreira, C.; Abreu, R. M. V.; Ramos, M. J.; Fernandes, P. A.; Martins, L. M.; Pereira, P. J. B.; Macedo-Ribeiro,
S.. "Molecular motion regulates the activity of the Mitochondrial Serine Protease HtrA2". Cell Death & Disease 8 (2017):
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000414022900040&KeyUID=WOS:000414022900040.
10.1038/cddis.2017.487
- Neves, R. P. P.; Fernandes, P. A.; Ramos, M. J.. "Mechanistic insights on the reduction of glutathione disulfide by protein
disulfide isomerase". Proceedings of the National Academy of Sciences of the United States of America 114 24 (2017):
E4724-E4733. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000403179300004&KeyUID=WOS:000403179300004.
10.1073/pnas.1618985114
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as a targeted therapy for cancer and viral infections". Expert Opinion on Therapeutic Patents 27 3 (2017): 283-297.
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10.1080/13543776.2017.1254194
- Medina, F. E.; Neves, R. P. P.; Ramos, M. J.; Fernandes, P. A.. "A QM/MM study of the reaction mechanism of human beta-ketoacyl
reductase". Physical Chemistry Chemical Physics 19 1 (2017): 347-355. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000391725300037&KeyUID=WOS:000391725300037.
10.1039/c6cp07014k
- Proença, C.; Freitas, M.; Ribeiro, D.; Oliveira, E.F.T.; Sousa, J.L.C.; Tomé, S.M.; Ramos, M.J.; et al. "a-Glucosidase inhibition
by flavonoids: an in vitro and in silico structure–activity relationship study". Journal of Enzyme Inhibition and Medicinal
Chemistry 32 1 (2017): 1216-1228. http://www.scopus.com/inward/record.url?eid=2-s2.0-85029757909&partnerID=MN8TOARS.
10.1080/14756366.2017.1368503
- Sousa, C.F.; Coimbra, J.T.S.; Gomes, I.; Franco, R.; Fernandes, P.A.; Gameiro, P.; Sousa, C. F.; Coimbra, J. T. S.; Fernandes,
P. A.. "The binding of free and copper-complexed fluoroquinolones to OmpF porins: an experimental and molecular docking study".
RSC Advances 7 17 (2017): 10009-10019. http://www.scopus.com/inward/record.url?eid=2-s2.0-85012008929&partnerID=MN8TOARS.
10.1039/C6RA26466B
- Ferreira, P; Sousa, SF; Fernandes, PA; Ramos, MJ. "Frontispiece: Improving the Catalytic Power of the DszD Enzyme for the
Biodesulfurization of Crude Oil and Derivatives". Chemistry – A European Journal (2017): https://www.authenticus.pt/P-00Z-K6H.
10.1002/chem.201786864
- Moorthy, Nshn; Sousa, S. F.; Ramos, M. J.; Fernandes, P. A.. "Binding mode of conformations and structure-based pharmacophore
development for farnesyltransferase inhibitors". Medicinal Chemistry Research 25 7 (2016): 1340-1357. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000378573400006&KeyUID=WOS:000378573400006.
10.1007/s00044-016-1578-y
- Cerqueira, Nmfsa; Oliveira, E. F.; Gesto, D. S.; Santos-Martins, D.; Moreira, C.; Moorthy, H. N.; Ramos, M. J.; Fernandes,
P. A.. "Cholesterol Biosynthesis: A Mechanistic Overview". Biochemistry 55 39 (2016): 5483-5506. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000384842100001&KeyUID=WOS:000384842100001.
10.1021/acs.biochem.6b00342
- Moreira, C.; Ramos, M. J.; Fernandes, P. A.. "Glutamine Synthetase Drugability beyond Its Active Site: Exploring Oligomerization
Interfaces and Pockets". Molecules 21 8 (2016): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000382334600067&KeyUID=WOS:000382334600067.
10.3390/molecules21081028
- Oliveira, E. F.; Cerqueira, Nmfsa; Ramos, M. J.; Fernandes, P. A.. "QM/MM study of the mechanism of reduction of 3-hydroxy-3-methylglutaryl
coenzyme A catalyzed by human HMG-CoA reductase". Catalysis Science & Technology 6 19 (2016): 7172-7185. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000384876400018&KeyUID=WOS:000384876400018.
10.1039/c6cy00356g
- Moreira, C.; Ramos, M. J.; Fernandes, P. A.. "Reaction Mechanism of Mycobacterium Tuberculosis Glutamine Synthetase Using
Quantum Mechanics/Molecular Mechanics Calculations". Chemistry-a European Journal 22 27 (2016): 9218-9225. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000380271100028&KeyUID=WOS:000380271100028.
10.1002/chem.201600305
- Llinas, P.; Chenon, M.; Nguyen, T. Q.; Moreira, C.; de Regibus, A.; Coquard, A.; Ramos, M. J.; et al. "Structure of a truncated
form of leucine zipper II of JIP3 reveals an unexpected antiparallel coiled-coil arrangement". Acta Crystallographica Section
F-Structural Biology Communications 72 (2016): 198-206. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000371619200006&KeyUID=WOS:000371619200006.
10.1107/s2053230x16001576
- Moniz, T.; Coimbra, J. T. S.; Bras, N. F.; Cunha-Silva, L.; Ramos, M. J.; Fernandes, P. A.; de Castro, B.; Rangel, M.. "Synthesis
and structural characterization, by spectroscopic and computational methods, of two fluorescent 3-hydroxy-4-pyridinone chelators
bearing sulphorhodamine B and naphthalene". Rsc Advances 6 5 (2016): 4200-4211. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000369508800094&KeyUID=WOS:000369508800094.
10.1039/c5ra23217a
- Oliveira, E. F.; Santos-Martins, D.; Ribeiro, A. M.; Bras, N. F.; Cerqueira, N. S.; Sousa, S. F.; Ramos, M. J.; Fernandes,
P. A.. "HMG-CoA Reductase inhibitors: an updated review of patents of novel compounds and formulations (2011-2015)". Expert
Opinion on Therapeutic Patents 26 11 (2016): 1257-1272. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000386784000004&KeyUID=WOS:000386784000004.
10.1080/13543776.2016.1216977
- Sousa, S. F.; Sousa, J. F. M.; Barbosa, A. C. C.; Ferreira, C. E.; Neves, R. P. P.; Ribeiro, A. J. M.; Fernandes, P. A.; Ramos,
M. J.. "Improving the Biodesulfurization of Crude Oil and Derivatives: A QM/MM Investigation of the Catalytic Mechanism of
NADH-FMN Oxidoreductase (DszD)". Journal of Physical Chemistry A 120 27 (2016): 5300-5306. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000379988900079&KeyUID=WOS:000379988900079.
10.1021/acs.jpca.6b01536
- Sousa, R. P.; Fernandes, P. A.; Ramos, M. J.; Bras, N. F.. "Insights into the reaction mechanism of 3-O-sulfotransferase through
QM/MM calculations". Physical Chemistry Chemical Physics 18 16 (2016): 11488-11496. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000374786300091&KeyUID=WOS:000374786300091.
10.1039/c5cp06224a
- Moorthy, Nshn; Sousa, S. F.; Ramos, M. J.; Fernandes, P. A.. "Molecular dynamic simulations and structure-based pharmacophore
development for farnesyltransferase inhibitors discovery". Journal of Enzyme Inhibition and Medicinal Chemistry 31
6 (2016): 1428-1442. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000385270300073&KeyUID=WOS:000385270300073.
10.3109/14756366.2016.1144593
- Bras, N. F.; Ferreira, P.; Calixto, A. R.; Jaspars, M.; Houssen, W.; Naismith, J. H.; Fernandes, P. A.; Ramos, M. J.. "The
Catalytic Mechanism of the Marine-Derived Macrocyclase PatGmac". Chemistry-a European Journal 22 37 (2016): 13089-13097.
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000383763200022&KeyUID=WOS:000383763200022.
10.1002/chem.201601670
- Neves, R. P. P.; Fernandes, P. A.; Ramos, M. J.. "Unveiling the Catalytic Mechanism of NADP(+)-Dependent Isocitrate Dehydrogenase
with QM/MM Calculations". Acs Catalysis 6 1 (2016): 357-368. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000367706800039&KeyUID=WOS:000367706800039.
10.1021/acscatal.5b01928
- Santos-Martins, D.; Fernandes, P. A.; Ramos, M. J.. "Calculation of distribution coefficients in the SAMPL5 challenge from
atomic solvation parameters and surface areas". Journal of Computer-Aided Molecular Design 30 11 (2016): 1079-1086.
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000391459000013&KeyUID=WOS:000391459000013.
10.1007/s10822-016-9951-y
- Brás, N.F.; Ferreira, P.; Calixto, A.R.; Jaspars, M.; Houssen, W.; Naismith, J.H.; Fernandes, P.A.; Ramos, M.J.. "Inside Cover:
The Catalytic Mechanism of the Marine-Derived Macrocyclase PatGmac (Chem. Eur. J. 37/2016)". Chemistry - A European Journal
22 37 (2016): 12946-12946. http://www.scopus.com/inward/record.url?eid=2-s2.0-84984941908&partnerID=MN8TOARS.
10.1002/chem.201603742
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10.24927/rce2015.037
- Pedro Fernandes. "Casa das Ci¿ncias: Futuro Incerto?". Revista de Ciência Elementar 3 1 (2015): https://doi.org/10.24927/rce2015.001.
10.24927/rce2015.001
- Pinto, Gaspar P.; Bras, Natercia F.; Perez, Marta A. S.; Fernandes, Pedro A.; Russo, Nino; Ramos, Maria J.; Toscano, Marirosa.
"Establishing the Catalytic Mechanism of Human Pancreatic alpha-Amylase with QM/MM Methods". Journal of Chemical Theory
and Computation 11 6 (2015): 2508-2516. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000356201700012&KeyUID=WOS:000356201700012.
10.1021/acs.jctc.5b00222
- Ribeiro, Antonio J. M.; Yang, Lifeng; Ramos, Maria J.; Fernandes, Pedro A.; Liang, Zhao-Xun; Hirao, Hajime. "Insight into
Enzymatic Nitrile Reduction: QM/MM Study of the Catalytic Mechanism of QueF Nitrile Reductase". Acs Catalysis 5 6 (2015):
3740-3751. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000355964300062&KeyUID=WOS:000355964300062.
10.1021/acscatal.5b00528
- Cerqueira, Nuno M. F. S. A.; Coelho, Catarina; Bras, Natercia F.; Fernandes, Pedro A.; Garattini, Enrico; Terao, Mineko; Romao,
Maria Joao; Ramos, Maria Joao. "Insights into the structural determinants of substrate specificity and activity in mouse aldehyde
oxidases". Journal of Biological Inorganic Chemistry 20 2 (2015): 209-217. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000350236100004&KeyUID=WOS:000350236100004.
10.1007/s00775-014-1198-2
- Moorthy, N. S. Hari Narayana; Cerqueira, Nuno M. F. S. A.; Ramos, Maria J.; Fernandes, Pedro A.. "Ligand based analysis on
HMG-CoA reductase inhibitors". Chemometrics and Intelligent Laboratory Systems 140 (2015): 102-116. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000349062500011&KeyUID=WOS:000349062500011.
10.1016/j.chemolab.2014.11.009
- Moreira, Irina S.; Martins, Joao M.; Coimbra, Joa T. S.; Ramos, Maria J.; Fernandes, Pedro A.. "A new scoring function for
protein-protein docking that identifies native structures with unprecedented accuracy". Physical Chemistry Chemical Physics
17 4 (2015): 2378-2387. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000346906700012&KeyUID=WOS:000346906700012.
10.1039/c4cp04688a
- Ribeiro, Antonio J. M.; Santos-Martins, Diogo; Russo, Nino; Rarnos, Maria J.; Fernandes, Pedro A.. "Enzymatic Flexibility
and Reaction Rate: A QM/MM Study of HIV-1 Protease". Acs Catalysis 5 9 (2015): 5617-5626. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000361089700073&KeyUID=WOS:000361089700073.
10.1021/acscatal.5b00759
- Sousa, Sergio F.; Ramos, Maria J.; Lim, Carmay; Fernandes, Pedro A.. "Relationship between Enzyme/Substrate Properties and
Enzyme Efficiency in Hydrolases". Acs Catalysis 5 10 (2015): 5877-5887. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000362391500023&KeyUID=WOS:000362391500023.
10.1021/acscatal.5b00923
- Shi, Yan X.; Liang, Rong Z.; Martin, Katherine A.; Weston, Nicholas; Gonzalez-Calera, Silvia; Ganguly, Rakesh; Li, Yongxin;
et al. "Synthesis and Hydrolytic Studies on the Air-Stable (4-CN-PhO)(E)P(mu-(NBu)-Bu-t) (2) (E = O, S, and Se) Cyclodiphosphazanes".
Inorganic Chemistry 54 13 (2015): 6423-6432. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000357705800044&KeyUID=WOS:000357705800044.
10.1021/acs.inorgchem.5b00735
- Cerqueira, Nuno M. F. S. A.; Gonzalez, Pablo J.; Fernandes, Pedro A.; Moura, Jose J. G.; Ramos, Maria Joao. "Periplasmic Nitrate
Reductase and Formate Dehydrogenase: Similar Molecular Architectures with Very Different Enzymatic Activities". Accounts
of Chemical Research 48 11 (2015): 2875-2884. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000365150500009&KeyUID=WOS:000365150500009.
10.1021/acs.accounts.5b00333
- Oliveira, Bruno L.; Morais, Mauricio; Mendes, Filipa; Moreira, Irina S.; Cordeiro, Carlos; Fernandes, Pedro A.; Ramos, Maria
J.; et al. "Re(I) and Tc(I) Complexes for Targeting Nitric Oxide Synthase: Influence of the Chelator in the Affinity for the
Enzyme". Chemical Biology & Drug Design 86 5 (2015): 1072-1086. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000365404100013&KeyUID=WOS:000365404100013.
10.1111/cbdd.12575
- Cerqueira, Nuno M. F. S. A.; Gesto, Diana; Oliveira, Eduardo F.; Santos-Martins, Diogo; Bras, Natercia F.; Sousa, Sergio F.;
Fernandes, Pedro A.; Ramos, Maria J.. "Receptor-based virtual screening protocol for drug discovery". Archives of Biochemistry
and Biophysics 582 (2015): 56-67. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000360781200007&KeyUID=WOS:000360781200007.
10.1016/j.abb.2015.05.011
- Pedro Fernandes. "II Encontro Casa das Ciências". Revista de Ciência Elementar 2 3 (2014): https://doi.org/10.24927/rce2014.051.
10.24927/rce2014.051
- Pinto, G.P.; Ribeiro, A.J.M.; Ramos, M.J.; Fernandes, P.A.; Toscano, M.; Russo, N.. "New insights in the catalytic mechanism
of tyrosine ammonia-lyase given by QM/MM and QM cluster models". Archives of Biochemistry and Biophysics (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84924860022&partnerID=MN8TOARS.
10.1016/j.abb.2015.03.002
- Moreira, I.S.; Ramos, R.M.; Martins, J.M.; Fernandes, P.A.; Ramos, M.J.. "Are hot-spots occluded from water?". Journal
of Biomolecular Structure and Dynamics 32 2 (2014): 186-197. http://www.scopus.com/inward/record.url?eid=2-s2.0-84889633435&partnerID=MN8TOARS.
10.1080/07391102.2012.758598
- Ngo, H.-P.-T.; Cerqueira, N.M.F.S.A.; Kim, J.-K.; Hong, M.-K.; Fernandes, P.A.; Ramos, M.J.; Kang, L.-W.. "PLP undergoes conformational
changes during the course of an enzymatic reaction". Acta Crystallographica Section D: Biological Crystallography 70
2 (2014): 596-606. http://www.scopus.com/inward/record.url?eid=2-s2.0-84894146310&partnerID=MN8TOARS.
10.1107/S1399004713031283
- Aranda, J.; Cerqueira, N.M.; Fernandes, P.A.; Roca, M.; Tuñon, I.; Ramos, M.J.. "The catalytic mechanism of carboxylesterases:
a computational study.". Biochemistry 53 36 (2014): 5820-5829. http://www.scopus.com/inward/record.url?eid=2-s2.0-84908352478&partnerID=MN8TOARS.
10.1021/bi500934j
- Coimbra, J.T.S.; Sousa, S.F.; Fernandes, P.A.; Rangel, M.; Ramos, M.J.. "Biomembrane simulations of 12 lipid types using the
general amber force field in a tensionless ensemble". Journal of Biomolecular Structure and Dynamics 32 1 (2014): 88-103.
http://www.scopus.com/inward/record.url?eid=2-s2.0-84889680410&partnerID=MN8TOARS.
10.1080/07391102.2012.750250
- Dourado, D.F.A.R.; Fernandes, P.A.; Mannervik, B.; Ramos, M.J.. "Isomerization of ¿5-androstene-3,17-dione into ¿4-androstene-3,17-dione
catalyzed by human glutathione transferase A3-3: A computational study identifies a dual role for glutathione". Journal
of Physical Chemistry A 118 31 (2014): 5790-5800. http://www.scopus.com/inward/record.url?eid=2-s2.0-84905718002&partnerID=MN8TOARS.
10.1021/jp410810q
- Brás, N.F.; Fernandes, P.A.; Ramos, M.J.. "Molecular dynamics studies on both bound and unbound renin protease". Journal
of Biomolecular Structure and Dynamics 32 3 (2014): 351-363. http://www.scopus.com/inward/record.url?eid=2-s2.0-84892981145&partnerID=MN8TOARS.
10.1080/07391102.2013.768553
- Silva, A.M.N.; Sousa, P.R.H.; Coimbra, J.T.S.; Brás, N.F.; Vitorino, R.; Fernandes, P.A.; Ramos, M.J.; Rangel, M.; Domingues,
P.. "The glycation site specificity of human serum transferrin is a determinant for transferrin's functional impairment under
elevated glycaemic conditions". Biochemical Journal 461 1 (2014): 33-42. http://www.scopus.com/inward/record.url?eid=2-s2.0-84902345071&partnerID=MN8TOARS.
10.1042/BJ20140133
- Neves, R.P.P.; Fernandes, P.A.; Varandas, A.J.C.; Ramos, M.J.. "Benchmarking of density functionals for the accurate description
of thiol-disulfide exchange". Journal of Chemical Theory and Computation 10 11 (2014): 4842-4856. http://www.scopus.com/inward/record.url?eid=2-s2.0-84909971050&partnerID=MN8TOARS.
10.1021/ct500840f
- Sousa, S.F.; Cerqueira, N.M.F.S.A.; Brás, N.F.; Fernandes, P.A.; Ramos, M.J.. "Enzymatic "tricks": Carboxylate shift and sulfur
shift". International Journal of Quantum Chemistry 114 19 (2014): 1253-1256. http://www.scopus.com/inward/record.url?eid=2-s2.0-84906310448&partnerID=MN8TOARS.
10.1002/qua.24689
- Martins, S.A.; Sousa, S.F.; Ramos, M.J.; Fernandes, P.A.. "Prediction of solvation free energies with thermodynamic integration
using the general Amber force field". Journal of Chemical Theory and Computation 10 8 (2014): 3570-3577. http://www.scopus.com/inward/record.url?eid=2-s2.0-84906272546&partnerID=MN8TOARS.
10.1021/ct500346y
- Calixto, A.R.; Brás, N.F.; Fernandes, P.A.; Ramos, M.J.. "Reaction mechanism of human renin studied by quantum mechanics/molecular
mechanics (QM/MM) calculations". ACS Catalysis 4 11 (2014): 3869-3876. http://www.scopus.com/inward/record.url?eid=2-s2.0-84910096204&partnerID=MN8TOARS.
10.1021/cs500497f
- Araújo, A.R.; Ribeiro, A.J.M.; Fernandes, P.A.; Ramos, M.J.. "Catalytic mechanism of retroviral integrase for the strand transfer
reaction explored by QM/MM calculations". Journal of Chemical Theory and Computation 10 12 (2014): 5458-5466. http://www.scopus.com/inward/record.url?eid=2-s2.0-84916882426&partnerID=MN8TOARS.
10.1021/ct500570g
- Coimbra, J.T.S.; Moniz, T.; Brás, N.F.; Ivanova, G.; Fernandes, P.A.; Ramos, M.J.; Rangel, M.. "Relevant interactions of antimicrobial
iron chelators and membrane models revealed by nuclear magnetic resonance and molecular dynamics simulations". Journal
of Physical Chemistry B 118 50 (2014): 14590-14601. http://www.scopus.com/inward/record.url?eid=2-s2.0-84919389836&partnerID=MN8TOARS.
10.1021/jp509491p
- Jarukanont, D.; Coimbra, J.T.S.; Bauerhenne, B.; Fernandes, P.A.; Patel, S.; Ramos, M.J.; Garcia, M.E.. "Biomolecular structure
manipulation using tailored electromagnetic radiation: A proof of concept on a simplified model of the active site of bacterial
DNA topoisomerase". Physical Chemistry Chemical Physics 16 39 (2014): 21768-21777. http://www.scopus.com/inward/record.url?eid=2-s2.0-84907833756&partnerID=MN8TOARS.
10.1039/c4cp02289k
- Coimbra, J.T.S.; Neves, R.P.P.; Passos, Ó.; Jarukanont, D.; Fernandes, P.A.; Patel, S.; Garcia, M.E.; Ramos, M.J.. "Influence
of the environment on protein bond energies". Chemical Physics Letters 615 (2014): 75-82. http://www.scopus.com/inward/record.url?eid=2-s2.0-84908192323&partnerID=MN8TOARS.
10.1016/j.cplett.2014.09.066
- Brás, N.F.; Fernandes, P.A.; Ramos, M.J.. "Discovery of new sites for drug binding to the hypertension-related renin-angiotensinogen
complex". Chemical Biology and Drug Design 83 4 (2014): 427-439. http://www.scopus.com/inward/record.url?eid=2-s2.0-84898939513&partnerID=MN8TOARS.
10.1111/cbdd.12258
- Brás, N.F.; Ribeiro, A.J.M.; Oliveira, M.; Paixão, N.M.; Tamames, J.A.; Fernandes, P.A.; Ramos, M.J.. "Analyses of cobalt-ligand
and potassium-ligand bond lengths in metalloproteins: Trends and patterns". Journal of Molecular Modeling 20 6 (2014):
http://www.scopus.com/inward/record.url?eid=2-s2.0-84901542884&partnerID=MN8TOARS.
10.1007/s00894-014-2271-z
- Ribeiro, J.V.; Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J.. "Chem-path-tracker: An automated tool to analyze chemical
motifs in molecular structures". Chemical Biology and Drug Design 84 1 (2014): 44-53. http://www.scopus.com/inward/record.url?eid=2-s2.0-84902827564&partnerID=MN8TOARS.
10.1111/cbdd.12349
- Moorthy, N.S.H.N.; Ramos, M.J.; Fernandes, P.A.. "Predictive QSAR models development and validation for human ether-a-go-go
related gene (hERG) blockers using newer tools". Journal of Enzyme Inhibition and Medicinal Chemistry 29 3 (2014):
317-324. http://www.scopus.com/inward/record.url?eid=2-s2.0-84886842373&partnerID=MN8TOARS.
10.3109/14756366.2013.779264
- Brás, N.F.; Fernandes, P.A.; Ramos, M.J.. "QM/MM study and MD simulations on the hypertension regulator angiotensin-converting
enzyme". ACS Catalysis 4 8 (2014): 2587-2597. http://www.scopus.com/inward/record.url?eid=2-s2.0-84905505163&partnerID=MN8TOARS.
10.1021/cs500093h
- Gesto, D.S.; Cerqueira, N.M.F.S.A.; Ramos, M.J.; Fernandes, P.A.. "Discovery of new druggable sites in the anti-cholesterol
target HMG-CoA reductase by computational alanine scanning mutagenesis". Journal of Molecular Modeling 20 4 (2014):
http://www.scopus.com/inward/record.url?eid=2-s2.0-84896563914&partnerID=MN8TOARS.
10.1007/s00894-014-2178-8
- Narayana Moorthy, N.S.H.; Martins, S.A.; Sousa, S.F.; Ramos, M.J.; Fernandes, P.A.. "Classification study of solvation free
energies of organic molecules using machine learning techniques". RSC Advances 4 106 (2014): 61624-61630. http://www.scopus.com/inward/record.url?eid=2-s2.0-84912036156&partnerID=MN8TOARS.
10.1039/c4ra07961b
- Hari Narayana Moorthy, N.S.; Pratheepa, V.; Ramos, M.J.; Vasconcelos, V.; Fernandes, P.A.. "Fused aryl-phenazines: Scaffold
for the development of bioactive molecules". Current Drug Targets 15 7 (2014): 681-688. http://www.scopus.com/inward/record.url?eid=2-s2.0-84904471837&partnerID=MN8TOARS.
10.2174/1389450115666140205152007
- Hong, M.-K.; Ribeiro, A.J.M.; Kim, J.-K.; Ngo, H.-P.-T.; Kim, J.; Lee, C.H.; Ahn, Y.-J.; et al. "Divalent metal ion-based
catalytic mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli". Acta Crystallographica Section D: Biological
Crystallography 70 5 (2014): 1297-1310. http://www.scopus.com/inward/record.url?eid=2-s2.0-84900416783&partnerID=MN8TOARS.
10.1107/S1399004714002570
- Brás, N.F.; Cerqueira, N.M.F.S.A.; Ramos, M.J.; Fernandes, P.A.. "Glycosidase inhibitors: A patent review (2008-2013)". Expert
Opinion on Therapeutic Patents 24 8 (2014): 857-874. http://www.scopus.com/inward/record.url?eid=2-s2.0-84904688162&partnerID=MN8TOARS.
10.1517/13543776.2014.916280
- Moorthy, N.S.H.N.; Brás, N.F.; Ramos, M.J.; Fernandes, P.A.. "Binding mode prediction and identification of new lead compounds
from natural products as renin and angiotensin converting enzyme inhibitors". RSC Advances 4 38 (2014): 19550-19568.
http://www.scopus.com/inward/record.url?eid=2-s2.0-84899808587&partnerID=MN8TOARS.
10.1039/c4ra00856a
- Pedro Fernandes. "Prémio Nobel da Química 2013". Revista de Ciência Elementar 1 1 (2013): https://doi.org/10.24927/rce2013.002.
10.24927/rce2013.002
- Moorthy, N.S.H.N.; Cerqueira, N.M.F.S.A.; Ramos, M.J.; Fernandes, P.A.. "Combined ligand and structure based binding mode
analysis of oxidosqualene cyclase inhibitors". RSC Advances 3 45 (2013): 23409-23422. http://www.scopus.com/inward/record.url?eid=2-s2.0-84886867161&partnerID=MN8TOARS.
10.1039/c3ra43670e
- Ribeiro, J.V.; Tamames, J.A.C.; Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J.. "Volarea - A bioinformatics tool to calculate
the surface area and the volume of molecular systems". Chemical Biology and Drug Design 82 6 (2013): 743-755. http://www.scopus.com/inward/record.url?eid=2-s2.0-84889887906&partnerID=MN8TOARS.
10.1111/cbdd.12197
- Oliveira, B.L.; Moreira, I.S.; Fernandes, P.A.; Ramos, M.J.; Santos, I.; Correia, J.D.G.. "Insights into the structural determinants
for selective inhibition of nitric oxide synthase isoforms". Journal of Molecular Modeling 19 4 (2013): 1537-1551.
http://www.scopus.com/inward/record.url?eid=2-s2.0-84876407327&partnerID=MN8TOARS.
10.1007/s00894-012-1677-8
- Moorthy, N.S.H.N.; Ramos, M.J.; Fernandes, P.A.. "Human ether-a-go-go-related gene channel blockers and its structural analysis
for drug design". Current Drug Targets 14 1 (2013): 102-113. http://www.scopus.com/inward/record.url?eid=2-s2.0-84876710977&partnerID=MN8TOARS.
- Martins, S.A.; Perez, M.A.S.; Moreira, I.S.; Sousa, S.F.; Ramos, M.J.; Fernandes, P.A.. "Computational alanine scanning mutagenesis:
MM-PBSA vs TI". Journal of Chemical Theory and Computation 9 3 (2013): 1311-1319. http://www.scopus.com/inward/record.url?eid=2-s2.0-84874848450&partnerID=MN8TOARS.
10.1021/ct4000372
- Moorthy, N.S.H.N.; Cerqueira, N.M.F.S.A.; Ramos, M.J.; Fernandes, P.A.. "Aryl-and heteroaryl-thiosemicarbazone derivatives
and their metal complexes: A pharmacological template". Recent Patents on Anti-Cancer Drug Discovery 8 2 (2013): 168-182.
http://www.scopus.com/inward/record.url?eid=2-s2.0-84875300425&partnerID=MN8TOARS.
10.2174/157489213805290583
- Sousa, S.F.; Ribeiro, A.J.M.; Coimbra, J.T.S.; Neves, R.P.P.; Martins, S.A.; Moorthy, N.S.H.N.; Fernandes, P.A.; Ramos, M.J..
"Protein-ligand docking in the new millennium - A retrospective of 10 years in the field". Current Medicinal Chemistry
20 18 (2013): 2296-2314. http://www.scopus.com/inward/record.url?eid=2-s2.0-84877933286&partnerID=MN8TOARS.
10.2174/0929867311320180002
- Neves, R.P.P.; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Parameters for molecular dynamics simulations of manganese-containing
metalloproteins". Journal of Chemical Theory and Computation 9 6 (2013): 2718-2732. http://www.scopus.com/inward/record.url?eid=2-s2.0-84879120460&partnerID=MN8TOARS.
10.1021/ct400055v
- Gesto, D.S.; Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J.. "Unraveling the enigmatic mechanism of l-asparaginase II
with QM/QM calculations". Journal of the American Chemical Society 135 19 (2013): 7146-7158. http://www.scopus.com/inward/record.url?eid=2-s2.0-84877811918&partnerID=MN8TOARS.
10.1021/ja310165u
- Ribeiro, A.J.M.; Ramos, M.J.; Fernandes, P.A.; Russo, N.. "A DFT study of the applicability of the charge balance model in
two-metal enzymes: The case of cAMP-dependent protein kinase". Chemical Physics Letters 571 (2013): 66-70. http://www.scopus.com/inward/record.url?eid=2-s2.0-84877833562&partnerID=MN8TOARS.
10.1016/j.cplett.2013.03.085
- Oliveira, B.L.; Moreira, I.S.; Fernandes, P.A.; Ramos, M.J.; Santos, I.; Correia, J.D.G.. "Theoretical studies on the binding
of rhenium(I) complexes to inducible nitric oxide synthase". Journal of Molecular Graphics and Modelling 45 (2013):
13-25. http://www.scopus.com/inward/record.url?eid=2-s2.0-84884558273&partnerID=MN8TOARS.
10.1016/j.jmgm.2013.07.007
- Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Gonzalez, P.J.; Moura, J.J.G.; Ramos, M.J.. "The sulfur shift: An activation mechanism
for periplasmic nitrate reductase and formate dehydrogenase". Inorganic Chemistry 52 19 (2013): 10766-10772. http://www.scopus.com/inward/record.url?eid=2-s2.0-84885114475&partnerID=MN8TOARS.
10.1021/ic3028034
- Ribeiro, A.J.M.; Ramos, M.J.; Fernandes, P.A.; Russo, N.. "Erratum: A DFT study of the applicability of the charge balance
model in two-metal enzymes: The case of cAMP-dependent protein kinase (Chemical Physics Letters (2012) 51:49 12242-12245)".
Chemical Physics Letters 579 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84880331802&partnerID=MN8TOARS.
10.1016/j.cplett.2013.06.024
- Sousa, S.F.; Pinto, G.R.P.; Ribeiro, A.J.M.; Coimbra, J.T.S.; Fernandes, P.A.; Ramos, M.J.. "Comparative analysis of the performance
of commonly available density functionals in the determination of geometrical parameters for copper complexes". Journal
of Computational Chemistry 34 24 (2013): 2079-2090. http://www.scopus.com/inward/record.url?eid=2-s2.0-84885957406&partnerID=MN8TOARS.
10.1002/jcc.23349
- Moorthy, N.S.H.N.; Cerqueira, N.M.F.S.A.; Ramos, M.J.; Fernandes, P.A.. "Development of ribonucleotide reductase inhibitor:
A review on structure activity relationships". Mini-Reviews in Medicinal Chemistry 13 13 (2013): 1862-1872. http://www.scopus.com/inward/record.url?eid=2-s2.0-84888027525&partnerID=MN8TOARS.
10.2174/13895575113136660090
- Moorthy, N.S.H.N.; Sousa, S.F.; Ramos, M.J.; Fernandes, P.A.. "Farnesyltransferase inhibitors: A comprehensive review based
on quantitative structural analysis". Current Medicinal Chemistry 20 38 (2013): 4888-4923. http://www.scopus.com/inward/record.url?eid=2-s2.0-84889569673&partnerID=MN8TOARS.
10.2174/09298673113206660262
- Ribeiro, A.J.; Alberto, M.E.; Ramos, M.J.; Fernandes, P.A.; Russo, N.. "The catalytic mechanism of protein phosphatase 5 established
by DFT calculations". Chemistry (Weinheim an der Bergstrasse, Germany) 19 42 (2013): 14081-14089. http://www.scopus.com/inward/record.url?eid=2-s2.0-84928700256&partnerID=MN8TOARS.
10.1002/chem.201301565
- Dourado, D.F.A.R.; Fernandes, P.A.; Ramos, M.J.; Mannervik, B.. "Mechanism of glutathione transferase P1-1-catalyzed activation
of the prodrug canfosfamide (TLK286, TELCYTA)". Biochemistry 52 45 (2013): 8069-8078. http://www.scopus.com/inward/record.url?eid=2-s2.0-84887597240&partnerID=MN8TOARS.
10.1021/bi4005705
- Sousa, S.F.; Coimbra, J.T.S.; Paramos, D.; Pinto, R.; Guimarães, R.S.; Teixeira, V.; Fernandes, P.A.; Ramos, M.J.. "Molecular
dynamics analysis of a series of 22 potential farnesyltransferase substrates containing a CaaX-motif". Journal of Molecular
Modeling 19 2 (2013): 673-688. http://www.scopus.com/inward/record.url?eid=2-s2.0-84877128216&partnerID=MN8TOARS.
10.1007/s00894-012-1590-1
- Moorthy, N.S.H.N.; Ramos, M.J.; Fernandes, P.A.. "QSAR and pharmacophore analysis of a series of piperidinyl urea derivatives
as hERG blockers and H3 antagonists". Current Drug Discovery Technologies 10 1 (2013): 47-58. http://www.scopus.com/inward/record.url?eid=2-s2.0-84875452236&partnerID=MN8TOARS.
- Silva, P.J.; Perez, M.A.S.; Brás, N.F.; Fernandes, P.A.; Ramos, M.J.. "Erratum to: Improving the study of proton transfers
between amino acid side chains in solution: Choosing appropriate DFT functionals and avoiding hidden pitfalls (Theor Chem
Acc, (2012) 131, 117, 10.1007/s00214-012-1179-x)". Theoretical Chemistry Accounts 132 2 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84875366125&partnerID=MN8TOARS.
10.1007/s00214-012-1307-7
- Moreira, I.S.; Martins, J.M.; Ramos, R.M.; Fernandes, P.A.; Ramos, M.J.. "Understanding the importance of the aromatic amino-acid
residues as hot-spots". Biochimica et Biophysica Acta - Proteins and Proteomics 1834 1 (2013): 404-414. http://www.scopus.com/inward/record.url?eid=2-s2.0-84871721814&partnerID=MN8TOARS.
10.1016/j.bbapap.2012.07.005
- Moorthy, N.S.H.N.; Ramos, M.J.; Fernandes, P.A.. "Studies on a-glucosidase inhibitors development: Magic molecules for the
treatment of carbohydrate mediated diseases". Mini-Reviews in Medicinal Chemistry 12 8 (2012): 713-720. http://www.scopus.com/inward/record.url?eid=2-s2.0-84862625361&partnerID=MN8TOARS.
10.2174/138955712801264837
- Zhang, W.; Dourado, D.F.A.R.; Fernandes, P.A.; Ramos, M.J.; Mannervik, B.. "Multidimensional epistasis and fitness landscapes
in enzyme evolution". Biochemical Journal 445 1 (2012): 39-46. http://www.scopus.com/inward/record.url?eid=2-s2.0-84862489556&partnerID=MN8TOARS.
10.1042/BJ20120136
- Moorthy, N.S.H.N.; Cerqueira, N.M.F.S.A.; Ramos, M.J.; Fernandes, P.A.. "QSAR and pharmacophore analysis of thiosemicarbazone
derivatives as ribonucleotide reductase inhibitors". Medicinal Chemistry Research 21 6 (2012): 739-746. http://www.scopus.com/inward/record.url?eid=2-s2.0-84861897147&partnerID=MN8TOARS.
10.1007/s00044-011-9580-x
- Moorthy, N.S.H.N.; Ramos, M.J.; Fernandes, P.A.. "Analysis of van der Waals surface area properties for human ether-a-go-go-related
gene blocking activity: Computational study on structurally diverse compounds". SAR and QSAR in Environmental Research
23 5-6 (2012): 521-536. http://www.scopus.com/inward/record.url?eid=2-s2.0-84864688102&partnerID=MN8TOARS.
10.1080/1062936X.2012.666264
- Moorthy, N.S.H.N.; Sousa, S.F.; Ramos, M.J.; Fernandes, P.A.. "In silico based structural analysis of some piperidine analogs
as farnesyltransferase inhibitors". Medicinal Chemistry 8 5 (2012): 853-864. http://www.scopus.com/inward/record.url?eid=2-s2.0-84865803335&partnerID=MN8TOARS.
10.2174/157340612802084171
- Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Computational enzymatic catalysis - Clarifying enzymatic mechanisms with the help
of computers". Physical Chemistry Chemical Physics 14 36 (2012): 12431-12441. http://www.scopus.com/inward/record.url?eid=2-s2.0-84865477079&partnerID=MN8TOARS.
10.1039/c2cp41180f
- De Rienzo, F.; Moura Barbosa, A.J.; Perez, M.A.S.; Fernandes, P.A.; Ramos, M.J.; Menziani, M.C.. "The extracellular subunit
interface of the 5-HT3 receptors: A computational alanine scanning mutagenesis study". Journal of Biomolecular Structure
and Dynamics 30 3 (2012): 280-298. http://www.scopus.com/inward/record.url?eid=2-s2.0-84863873134&partnerID=MN8TOARS.
10.1080/07391102.2012.680029
- Ribeiro, A.J.M.; Ramos, M.J.; Fernandes, P.A.. "The catalytic mechanism of HIV-1 integrase for DNA 3'-end processing established
by QM/MM calculations". Journal of the American Chemical Society 134 32 (2012): 13436-13447. http://www.scopus.com/inward/record.url?eid=2-s2.0-84865142881&partnerID=MN8TOARS.
10.1021/ja304601k
- Narayana Moorthy, N.S.H.; Ramos, M.J.; Fernandes, P.A.. "Structural analysis of structurally diverse a-glucosidase inhibitors
for active site feature analysis". Journal of Enzyme Inhibition and Medicinal Chemistry 27 5 (2012): 649-657. http://www.scopus.com/inward/record.url?eid=2-s2.0-84866120433&partnerID=MN8TOARS.
10.3109/14756366.2011.605359
- Moorthy, N.S.H.N.; Brás, N.F.; Ramos, M.J.; Fernandes, P.A.. "Virtual screening and QSAR study of some pyrrolidine derivatives
as a-mannosidase inhibitors for binding feature analysis". Bioorganic and Medicinal Chemistry 20 24 (2012): 6945-6959.
http://www.scopus.com/inward/record.url?eid=2-s2.0-84870054757&partnerID=MN8TOARS.
10.1016/j.bmc.2012.10.011
- Brás, N.F.; Ramos, M.J.; Fernandes, P.A.. "The catalytic mechanism of mouse renin studied with QM/MM calculations". Physical
Chemistry Chemical Physics 14 36 (2012): 12605-12613. http://www.scopus.com/inward/record.url?eid=2-s2.0-84865447106&partnerID=MN8TOARS.
10.1039/c2cp41422h
- Ribeiro, J.V.; Cerqueira, N.M.F.S.A.; Moreira, I.S.; Fernandes, P.A.; Ramos, M.J.. "CompASM: An Amber-VMD alanine scanning
mutagenesis plug-in". Theoretical Chemistry Accounts 131 10 (2012): 1-7. http://www.scopus.com/inward/record.url?eid=2-s2.0-84866688979&partnerID=MN8TOARS.
10.1007/s00214-012-1271-2
- Narayana Moorthy, N.S.H.; Cerqueira, N.S.; Ramos, M.J.; Fernandes, P.A.. "QSAR analysis of 2-benzoxazolyl hydrazone derivatives
for anticancer activity and its possible target prediction". Medicinal Chemistry Research 21 2 (2012): 133-144. http://www.scopus.com/inward/record.url?eid=2-s2.0-84861888793&partnerID=MN8TOARS.
10.1007/s00044-010-9510-3
- Moorthy, N.S.H.N.; Ramos, M.J.; Fernandes, P.A.. "Structural analysis of 2-piperidin-4-yl-actamide derivatives for hERG blocking
and MCH R1 antagonistic activities". Current Drug Discovery Technologies 9 1 (2012): 25-38. http://www.scopus.com/inward/record.url?eid=2-s2.0-84858269405&partnerID=MN8TOARS.
10.2174/157016312799304543
- Narayana Moorthy, N.S.H.; Ramos, M.J.; Fernandes, P.A.. "Comparative structural analysis of a-glucosidase inhibitors on difference
species: A computational study". Archiv der Pharmazie 345 4 (2012): 265-274. http://www.scopus.com/inward/record.url?eid=2-s2.0-84859715389&partnerID=MN8TOARS.
10.1002/ardp.201100047
- Silva, P.J.; Perez, M.A.S.; Brás, N.F.; Fernandes, P.A.; Ramos, M.J.. "Improving the study of proton transfers between amino
acid side chains in solution: Choosing appropriate DFT functionals and avoiding hidden pitfalls". Theoretical Chemistry
Accounts 131 3 (2012): 1-6. http://www.scopus.com/inward/record.url?eid=2-s2.0-84857467426&partnerID=MN8TOARS.
10.1007/s00214-012-1179-x
- Gesto, D.S.; Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J.. "Gemcitabine: A critical nucleoside for cancer therapy".
Current Medicinal Chemistry 19 7 (2012): 1076-1087. http://www.scopus.com/inward/record.url?eid=2-s2.0-84858173640&partnerID=MN8TOARS.
10.2174/092986712799320682
- Salome, PMP; Malaquias, J; Fernandes, PA; Ferreira, MS; da Cunha, AF; Leitao, JP; Gonzalez, JC; Matinaga, FM. "Growth and
characterization of Cu2ZnSn(S,Se)(4) thin films for solar cells". SOLAR ENERGY MATERIALS AND SOLAR CELLS (2012): https://www.authenticus.pt/P-002-9SV.
10.1016/j.solmat.2012.02.031
- Oliveira, E.F.; Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J.. "Mechanism of formation of the internal aldimine in pyridoxal
5'-phosphate-dependent enzymes". Journal of the American Chemical Society 133 39 (2011): 15496-15505. http://www.scopus.com/inward/record.url?eid=2-s2.0-80053318335&partnerID=MN8TOARS.
10.1021/ja204229m
- Moorthy, N.S.H.N.; Ramos, M.J.; Fernandes, P.A.. "HERG binding feature analysis of structurally diverse compounds by QSAR
and fragmental analysis". RSC Advances 1 6 (2011): 1126-1136. http://www.scopus.com/inward/record.url?eid=2-s2.0-84858190134&partnerID=MN8TOARS.
10.1039/c1ra00131k
- Neves, A.R.; Fernandes, P.A.; Ramos, M.J.. "The accuracy of density functional theory in the description of cation-p and p-hydrogen
bond interactions". Journal of Chemical Theory and Computation 7 7 (2011): 2059-2067. http://www.scopus.com/inward/record.url?eid=2-s2.0-79960246616&partnerID=MN8TOARS.
10.1021/ct2001667
- Narayana Moorthy, N.S.H.; Sousa, S.F.; Ramos, M.J.; Fernandes, P.A.. "In silico-based structural analysis of arylthiophene
derivatives for FTase inhibitory activity, hERG, and other toxic effects". Journal of Biomolecular Screening 16 9 (2011):
1037-1046. http://www.scopus.com/inward/record.url?eid=2-s2.0-80053498208&partnerID=MN8TOARS.
10.1177/1087057111414899
- Hari Narayana Moorthy, N.S.; Ramos, M.J.; Fernandes, P.A.. "Topological, hydrophobicity, and other descriptors on a-glucosidase
inhibition: A QSAR study on xanthone derivatives". Journal of Enzyme Inhibition and Medicinal Chemistry 26 6 (2011):
755-766. http://www.scopus.com/inward/record.url?eid=2-s2.0-81355149312&partnerID=MN8TOARS.
10.3109/14756366.2010.549089
- Brás, N.F.; Perez, M.A.S.; Fernandes, P.A.; Silva, P.J.; Ramos, M.J.. "Accuracy of density functionals in the prediction of
electronic proton affinities of amino acid side chains". Journal of Chemical Theory and Computation 7 12 (2011): 3898-3908.
http://www.scopus.com/inward/record.url?eid=2-s2.0-83455218477&partnerID=MN8TOARS.
10.1021/ct200309v
- Moorthy, N.S.H.N.; Ramos, M.J.; Fernandes, P.A.. "Analysis of the a-glucosidase inhibitory activity of chromenone derivatives
based on their molecular features: A computational study". Medicinal Chemistry 7 6 (2011): 526-533. http://www.scopus.com/inward/record.url?eid=2-s2.0-80755125976&partnerID=MN8TOARS.
- Hari Narayana Moorthy, N.S.; Sousa, S.F.; Ramos, M.J.; Fernandes, P.A.. "Structural feature study of benzofuran derivatives
as farnesyltransferase inhibitors". Journal of Enzyme Inhibition and Medicinal Chemistry 26 6 (2011): 777-791. http://www.scopus.com/inward/record.url?eid=2-s2.0-81355138323&partnerID=MN8TOARS.
10.3109/14756366.2011.552885
- Perez, M.A.S.; Sousa, S.F.; Oliveira, E.F.T.; Fernandes, P.A.; Ramos, M.J.. "Detection of farnesyltransferase interface hot
spots through computational alanine scanning mutagenesis". Journal of Physical Chemistry B 115 51 (2011): 15339-15354.
http://www.scopus.com/inward/record.url?eid=2-s2.0-84255176172&partnerID=MN8TOARS.
10.1021/jp205481y
- Moorthy, N.S.H.N.; Ramos, M.J.; Fernandes, P.A.. "Structural analysis of a-glucosidase inhibitors by validated QSAR models
using topological and hydrophobicity based descriptors". Chemometrics and Intelligent Laboratory Systems 109 2 (2011):
101-112. http://www.scopus.com/inward/record.url?eid=2-s2.0-80055094177&partnerID=MN8TOARS.
10.1016/j.chemolab.2011.02.010
- Passos, O.; Fernandes, P.A.; Ramos, M.J.. "QM/MM study of the catalytic mechanism of GalNAc removal from GM2 ganglioside catalyzed
by human ß-hexosaminidaseA". Journal of Physical Chemistry B 115 49 (2011): 14751-14759. http://www.scopus.com/inward/record.url?eid=2-s2.0-83455201696&partnerID=MN8TOARS.
10.1021/jp205826n
- Hari Narayana Moorthy, N.S.; Ramos, M.J.; Fernandes, P.A.. "QSAR analysis of isosteviol derivatives as a-glucosidase inhibitors
with element count and other descriptors". Letters in Drug Design and Discovery 8 1 (2011): 14-25. http://www.scopus.com/inward/record.url?eid=2-s2.0-78650861840&partnerID=MN8TOARS.
10.2174/157018011793663859
- Carvalho, A.T.P.; Fernandes, P.A.; Ramos, M.J.. "The catalytic mechanism of RNA polymerase II". Journal of Chemical Theory
and Computation 7 4 (2011): 1177-1188. http://www.scopus.com/inward/record.url?eid=2-s2.0-79954471369&partnerID=MN8TOARS.
10.1021/ct100579w
- Passos, Ó.; Fernandes, P.A.; Ramos, M.J.. "Theoretical insights into the catalytic mechanism of ß-hexosaminidase". Theoretical
Chemistry Accounts 129 1 (2011): 119-129. http://www.scopus.com/inward/record.url?eid=2-s2.0-79954633470&partnerID=MN8TOARS.
10.1007/s00214-011-0904-1
- Narayana Moorthy, N.S.H.; Ramos, M.J.; Fernandes, P.A.. "Prediction of the relationship between the structural features of
andrographolide derivatives and aî±-glucosidase inhibitory activity: A quantitative structure-activity relationship (QSAR)
Study". Journal of Enzyme Inhibition and Medicinal Chemistry 26 1 (2011): 78-87. http://www.scopus.com/inward/record.url?eid=2-s2.0-79851474038&partnerID=MN8TOARS.
10.3109/14756361003724760
- Oliveira, J.; Petrov, V.; Parola, A.J.; Pina, F.; Azevedo, J.; Teixeira, N.; Brás, N.F.; et al. "Chemical behavior of methylpyranomalvidin-3-o-glucoside
in aqueous solution studied by NMR and UV-visible spectroscopy". Journal of Physical Chemistry B 115 6 (2011): 1538-1545.
http://www.scopus.com/inward/record.url?eid=2-s2.0-79951538171&partnerID=MN8TOARS.
10.1021/jp110593c
- Brás, N.F.; Cruz, L.; Fernandes, P.A.; De Freitas, V.; Ramos, M.J.. "Conformational study of two diasteroisomers of vinylcatechin
dimers in a methanol solution". International Journal of Quantum Chemistry 111 7-8 (2011): 1498-1510. http://www.scopus.com/inward/record.url?eid=2-s2.0-79953239442&partnerID=MN8TOARS.
10.1002/qua.22631
- Sousa, S.F.; Tamames, B.; Fernandes, P.A.; Ramos, M.J.. "Detailed atomistic analysis of the HIV-1 protease interface". Journal
of Physical Chemistry B 115 21 (2011): 7045-7057. http://www.scopus.com/inward/record.url?eid=2-s2.0-79957584233&partnerID=MN8TOARS.
10.1021/jp200075s
- Cerqueira, N.M.F.S.A.; Ribeiro, J.; Fernandes, P.A.; Ramos, M.J.. "VsLab - An implementation for virtual high-throughput screening
using AutoDock and VMD". International Journal of Quantum Chemistry 111 6 (2011): 1208-1212. http://www.scopus.com/inward/record.url?eid=2-s2.0-79952168691&partnerID=MN8TOARS.
10.1002/qua.22738
- Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J.. "Computational mechanistic studies addressed to the transimination reaction
present in all pyridoxal 5'-phosphate-requiring enzymes". Journal of Chemical Theory and Computation 7 5 (2011): 1356-1368.
http://www.scopus.com/inward/record.url?eid=2-s2.0-79955900191&partnerID=MN8TOARS.
10.1021/ct1002219
- Rodriguez, E; Azevedo, R; Fernandes, P; Santos, C. "Cr(VI) Induces DNA Damage, Cell Cycle Arrest and Polyploidization: A How
Cytometric and Comet Assay Study in Pisum sativum". CHEMICAL RESEARCH IN TOXICOLOGY (2011): https://www.authenticus.pt/P-002-Q1A.
10.1021/tx2001465
- Ribeiro, A.J.M.; Ramos, M.J.; Fernandes, P.A.. "Benchmarking of DFT functionals for the hydrolysis of phosphodiester bonds".
Journal of Chemical Theory and Computation 6 8 (2010): 2281-2292. http://www.scopus.com/inward/record.url?eid=2-s2.0-77955561344&partnerID=MN8TOARS.
10.1021/ct900649e
- Perez, M.A.S.; Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J.. "Ribonucleotide reductase: A mechanistic portrait of substrate
analogues inhibitors". Current Medicinal Chemistry 17 26 (2010): 2854-2872. http://www.scopus.com/inward/record.url?eid=2-s2.0-77955606286&partnerID=MN8TOARS.
10.2174/092986710792065054
- Sousa, S.F.; Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J.. "Virtual screening in drug design and development". Combinatorial
Chemistry and High Throughput Screening 13 5 (2010): 442-453. http://www.scopus.com/inward/record.url?eid=2-s2.0-77955767207&partnerID=MN8TOARS.
10.2174/138620710791293001
- Brás, N.F.; Gonçalves, R.; Fernandes, P.A.; Mateus, N.; Ramos, M.J.; De Freitas, V.. "Understanding the binding of procyanidins
to pancreatic elastase by experimental and computational methods". Biochemistry 49 25 (2010): 5097-5108. http://www.scopus.com/inward/record.url?eid=2-s2.0-77953906402&partnerID=MN8TOARS.
10.1021/bi100410q
- Dourado, D.F.A.R.; Fernandes, P.A.; Ramos, M.J.. "Glutathione transferase classes alpha, Pi, and Mu: GSH activation mechanism".
Journal of Physical Chemistry B 114 40 (2010): 12972-12980. http://www.scopus.com/inward/record.url?eid=2-s2.0-77957825421&partnerID=MN8TOARS.
10.1021/jp1053875
- Perez, M.A.S.; Fernandes, P.A.; Ramos, M.J.. "Understanding the mechanism for Ribonucleotide reductase inactivation by 2'-
Deoxy-2'-methylenecytidine-5'-diphosphate". Journal of Chemical Theory and Computation 6 9 (2010): 2770-2781. http://www.scopus.com/inward/record.url?eid=2-s2.0-77956594850&partnerID=MN8TOARS.
10.1021/ct1002175
- Brás, N.F.; Gonçalves, R.; Mateus, N.; Fernandes, P.A.; Ramos, M.J.; De Freitas, V.. "Inhibition of pancreatic elastase by
polyphenolic compounds". Journal of Agricultural and Food Chemistry 58 19 (2010): 10668-10676. http://www.scopus.com/inward/record.url?eid=2-s2.0-78049265413&partnerID=MN8TOARS.
10.1021/jf1017934
- Marques, A.T.; Fernandes, P.A.; Ramos, M.J.. "Structural analysis of ABAD point mutations causing 2-methyl-3- hydroxylbutyryl-coA
deficiency". International Journal of Quantum Chemistry 110 1 (2010): 148-160. http://www.scopus.com/inward/record.url?eid=2-s2.0-73849124964&partnerID=MN8TOARS.
10.1002/qua.22091
- Moreira, I.S.; Fernandes, P.A.; Ramos, M.J.. "Protein-protein docking dealing with the unknown". Journal of Computational
Chemistry 31 2 (2010): 317-342. http://www.scopus.com/inward/record.url?eid=2-s2.0-76149086786&partnerID=MN8TOARS.
10.1002/jcc.21276
- Perez, M.A.S.; Fernandes, P.A.; Ramos, M.J.. "Substrate recognition in HIV-1 protease: A computational study". Journal
of Physical Chemistry B 114 7 (2010): 2525-2532. http://www.scopus.com/inward/record.url?eid=2-s2.0-77249136920&partnerID=MN8TOARS.
10.1021/jp910958u
- Brás, N.F.; Ramos, M.J.; Fernandes, P.A.. "DFT studies on the ß-glycosidase catalytic mechanism: The deglycosylation step".
Journal of Molecular Structure: THEOCHEM 946 1-3 (2010): 125-133. http://www.scopus.com/inward/record.url?eid=2-s2.0-77649190284&partnerID=MN8TOARS.
10.1016/j.theochem.2009.08.039
- Dourado, D.F.A.R.; Fernandes, P.A.; Mannervik, B.; Ramos, M.J.. "Glutathione transferase A1-1: Catalytic importance of arginine
15". Journal of Physical Chemistry B 114 4 (2010): 1690-1697. http://www.scopus.com/inward/record.url?eid=2-s2.0-75749092981&partnerID=MN8TOARS.
10.1021/jp908251z
- Bráa, N.F.; Fernandes, P.A.; Ramos, M.J.. "QM/MM studies on the ß-galactosidase catalytic mechanism: Hydrolysis and transglycosylation
reactions". Journal of Chemical Theory and Computation 6 2 (2010): 421-433. http://www.scopus.com/inward/record.url?eid=2-s2.0-77950130195&partnerID=MN8TOARS.
10.1021/ct900530f
- Moura-Tamames, S.A.; Ramos, M.J.; Fernandes, P.A.. "Modelling ß-1,3-exoglucanase-saccharide interactions: Structure of the
enzyme-substrate complex and enzyme binding to the cell wall". Journal of Molecular Graphics and Modelling 27 8 (2009):
908-920. http://www.scopus.com/inward/record.url?eid=2-s2.0-67349243347&partnerID=MN8TOARS.
10.1016/j.jmgm.2009.01.007
- Dourado, D.F.A.R.; Fernandes, P.A.; Ramos, M.J.. "Glutathione transferase A1-1: Catalytic role of water". Theoretical Chemistry
Accounts 124 1-2 (2009): 71-83. http://www.scopus.com/inward/record.url?eid=2-s2.0-70449529533&partnerID=MN8TOARS.
10.1007/s00214-009-0582-4
- Sousa, S.F.; Fernandes, P.A.; Rãmos, M.J.. "The search for the mechanism of the reaction catalyzed by farnesyltransferase".
Chemistry - A European Journal 15 17 (2009): 4243-4247. http://www.scopus.com/inward/record.url?eid=2-s2.0-65349137563&partnerID=MN8TOARS.
10.1002/chem.200802745
- Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Molecular dynamics simulations on the critical states of the farnesyltransferase
enzyme". Bioorganic and Medicinal Chemistry 17 9 (2009): 3369-3378. http://www.scopus.com/inward/record.url?eid=2-s2.0-65249179022&partnerID=MN8TOARS.
10.1016/j.bmc.2009.03.055
- Sousa, S.F.; Lopes, A.B.; Fernandes, P.A.; Ramos, M.J.. "The Zinc proteome: A tale of stability and functionality". Dalton
Transactions 38 (2009): 7946-7956. http://www.scopus.com/inward/record.url?eid=2-s2.0-70349310441&partnerID=MN8TOARS.
10.1039/b904404c
- Cerqueira, N.M.; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Virtual screening of compound libraries.". Methods in molecular
biology (Clifton, N.J.) 572 (2009): 57-70. http://www.scopus.com/inward/record.url?eid=2-s2.0-79952110876&partnerID=MN8TOARS.
10.1007/978-1-60761-244-5_4
- Sousa, S.F.; Cerqueira, N.M.F.S.A.; Perez, M.A.S.; Moreira, I.S.; Ribeiro, A.J.M.; Neves, A.R.A.P.; Ramos, M.J.; Fernandes,
P.A.. "Recent advances on computational proteomics". World Academy of Science, Engineering and Technology 56 (2009):
376-386. http://www.scopus.com/inward/record.url?eid=2-s2.0-78651571830&partnerID=MN8TOARS.
- Marques, A.T.; Fernandes, P.A.; Ramos, M.J.. "ABAD: A potential therapeutic target for Aß-induced mitochondrial dysfunction
in Alzheimer's disease". Mini-Reviews in Medicinal Chemistry 9 8 (2009): 1002-1008. http://www.scopus.com/inward/record.url?eid=2-s2.0-70349090165&partnerID=MN8TOARS.
- Sousa, S.F.; Carvalho, E.S.; Ferreira, D.M.; Tavares, I.S.; Fernandes, P.A.; Ramos, M.J.; Gomes, J.A.N.F.. "Comparative analysis
of the performance of commonly available density functionals in the determination of geometrical parameters for zinc complexes".
Journal of Computational Chemistry 30 16 (2009): 2752-2763. http://www.scopus.com/inward/record.url?eid=2-s2.0-70349932424&partnerID=MN8TOARS.
10.1002/jcc.21304
- Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Gas-phase geometry optimization of biological molecules as a reasonable alternative
to a continuum environment description: Fact, myth, or fiction?". Journal of Physical Chemistry A 113 52 (2009): 14231-14236.
http://www.scopus.com/inward/record.url?eid=2-s2.0-73949129042&partnerID=MN8TOARS.
10.1021/jp902213t
- Brás, N.F.; Fernandes, P.A.; Ramos, M.J.. "Docking and molecular dynamics studies on the stereoselectivity in the enzymatic
synthesis of carbohydrates". Theoretical Chemistry Accounts 122 5-6 (2009): 283-296. http://www.scopus.com/inward/record.url?eid=2-s2.0-64149094355&partnerID=MN8TOARS.
10.1007/s00214-009-0507-2
- Carvalho, A.T.P.; Fernandes, P.A.; Swart, M.; Van Stralen, J.N.P.; Bickelhaupt, F.M.; Ramos, M.J.. "Role of the variable active
site residues in the function of thioredoxin family oxidoreductases". Journal of Computational Chemistry 30 5 (2009):
710-724. http://www.scopus.com/inward/record.url?eid=2-s2.0-64549135410&partnerID=MN8TOARS.
10.1002/jcc.21086
- Cerqueira, N.M.F.S.A.; Bras, N.F.; Fernandes, P.A.; Ramos, M.J.. "MADAMM: A multistaged docking with an automated molecular
modeling protocol". Proteins: Structure, Function and Bioinformatics 74 1 (2009): 192-206. http://www.scopus.com/inward/record.url?eid=2-s2.0-58949084789&partnerID=MN8TOARS.
10.1002/prot.22146
- Cruz, L.; Brás, N.F.; Teixeira, N.; Fernandes, A.N.A.; Mateus, N.; Ramos, M.J.; Rodríguez-Borges, J.; De Freitas, V.. "Synthesis
and structural characterization of two diasteroisomers of vinylcatechin dimers". Journal of Agricultural and Food Chemistry
57 21 (2009): 10341-10348. http://www.scopus.com/inward/record.url?eid=2-s2.0-70449120689&partnerID=MN8TOARS.
10.1021/jf901608n
- Ramos, M.J.; Fernandes, P.A.. "Computational enzymatic catalysis". Accounts of Chemical Research 41 6 (2008): 689-698.
http://www.scopus.com/inward/record.url?eid=2-s2.0-47249103804&partnerID=MN8TOARS.
10.1021/ar7001045
- Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Farnesyltransferase inhibitors: A detailed chemical view on an elusive biological
problem". Current Medicinal Chemistry 15 15 (2008): 1478-1492. http://www.scopus.com/inward/record.url?eid=2-s2.0-47349089381&partnerID=MN8TOARS.
10.2174/092986708784638825
- Martins, S.; Ramos, M.J.; Fernandes, P.A.. "The current status of the NNRTI family of antiretrovirals used in the HAART regime
against HIV infection". Current Medicinal Chemistry 15 11 (2008): 1083-1095. http://www.scopus.com/inward/record.url?eid=2-s2.0-48949117560&partnerID=MN8TOARS.
10.2174/092986708784221467
- Viegas, A.; Brás, N.F.; Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Prates, J.A.M.; Fontes, C.M.G.A.; Bruix, M.; et al. "Molecular
determinants of ligand specificity in family 11 carbohydrate binding modules - An NMR, X-ray crystallography and computational
chemistry approach". FEBS Journal 275 10 (2008): 2524-2535. http://www.scopus.com/inward/record.url?eid=2-s2.0-42649116746&partnerID=MN8TOARS.
10.1111/j.1742-4658.2008.06401.x
- Dourado, D.F.A.R.; Fernandes, P.A.; Ramos, M.J.. "Mammalian cytosolic glutathione transferases". Current Protein and Peptide
Science 9 4 (2008): 325-337. http://www.scopus.com/inward/record.url?eid=2-s2.0-49249135353&partnerID=MN8TOARS.
10.2174/138920308785132677
- Brás, N.F.; Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J.. "Carbohydrate-binding modules from family 11: Understanding
the binding mode of polysaccharides". International Journal of Quantum Chemistry 108 11 (2008): 2030-2040. http://www.scopus.com/inward/record.url?eid=2-s2.0-47549090465&partnerID=MN8TOARS.
10.1002/qua.21755
- Moreira, I.S.; Fernandes, P.A.; Ramos, M.J.. "Protein-protein recognition: A computational mutagenesis study of the MDM2-P53
complex". Theoretical Chemistry Accounts 120 4-6 (2008): 533-542. http://www.scopus.com/inward/record.url?eid=2-s2.0-45449099914&partnerID=MN8TOARS.
10.1007/s00214-008-0432-9
- Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Enzyme flexibility and the catalytic mechanism of farnesyltransferase: Targeting
the relation". Journal of Physical Chemistry B 112 29 (2008): 8681-8691. http://www.scopus.com/inward/record.url?eid=2-s2.0-49149110925&partnerID=MN8TOARS.
10.1021/jp711214j
- Dourado, D.F.A.R.; Fernandes, P.A.; Mannervik, B.; Ramos, M.J.. "Glutathione transferase: New model for glutathione activation".
Chemistry - A European Journal 14 31 (2008): 9591-9598. http://www.scopus.com/inward/record.url?eid=2-s2.0-55049084123&partnerID=MN8TOARS.
10.1002/chem.200800946
- Marques, A.T.; Fernandes, P.A.; Ramos, M.J.. "Molecular dynamics simulations of the amyloid-beta binding alcohol dehydrogenase
(ABAD) enzyme". Bioorganic and Medicinal Chemistry 16 21 (2008): 9511-9518. http://www.scopus.com/inward/record.url?eid=2-s2.0-53849140775&partnerID=MN8TOARS.
10.1016/j.bmc.2008.09.043
- Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Molecular dynamics analysis of farnesyltransferase: A closer look into the amino
acid behavior". International Journal of Quantum Chemistry 108 11 (2008): 1939-1950. http://www.scopus.com/inward/record.url?eid=2-s2.0-47549102060&partnerID=MN8TOARS.
10.1002/qua.21713
- Marques, A.T.; Antunes, A.; Fernandes, P.A.; Ramos, M.J.. "Computational optimization of AG18051 inhibitor for amyloid-ß binding
alcohol dehydrogenase enzyme". International Journal of Quantum Chemistry 108 11 (2008): 1982-1991. http://www.scopus.com/inward/record.url?eid=2-s2.0-47549087365&partnerID=MN8TOARS.
10.1002/qua.21716
- Brás, N.F.; Moura-Tamames, S.A.; Fernandes, P.A.; Ramos, M.J.. "Mechanistic studies on the formation of glycosidase-substrate
and glycosidase-inhibitor covalent intermediates". Journal of Computational Chemistry 29 15 (2008): 2565-2574. http://www.scopus.com/inward/record.url?eid=2-s2.0-55349124348&partnerID=MN8TOARS.
10.1002/jcc.21013
- Carvalho, A.T.P.; Swart, M.; Van Straten, J.N.P.; Fernandes, P.A.; Ramos, M.J.; Bickelhaupt, F.M.. "Mechanism of thioredoxin-catalyzed
disulfide reduction. Activation of the buried thiol and role of the variable active-site residues". Journal of Physical
Chemistry B 112 8 (2008): 2511-2523. http://www.scopus.com/inward/record.url?eid=2-s2.0-40549093328&partnerID=MN8TOARS.
10.1021/jp7104665
- Moreira, I.S.; Fernandes, P.A.; Ramos, M.J.. "Computational alanine scanning mutagenesis - An improved methodological approach".
Journal of Computational Chemistry 28 3 (2007): 644-654. http://www.scopus.com/inward/record.url?eid=2-s2.0-33847650393&partnerID=MN8TOARS.
10.1002/jcc.20566
- Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "The carboxylate shift in zinc enzymes: A computational study". Journal of the
American Chemical Society 129 5 (2007): 1378-1385. http://www.scopus.com/inward/record.url?eid=2-s2.0-33846840870&partnerID=MN8TOARS.
10.1021/ja067103n
- Moreira, I.S.; Fernandes, P.A.; Ramos, M.J.. "Hot spot computational identification: Application to the complex formed between
the hen egg white lysozyme (HEL) and the antibody HyHEL-10". International Journal of Quantum Chemistry 107 2 (2007):
299-310. http://www.scopus.com/inward/record.url?eid=2-s2.0-33845995126&partnerID=MN8TOARS.
10.1002/qua.21193
- Carvalho, A.T.P.; Fernandes, P.A.; Ramos, M.J.. "Parameterization of AZT - A widely used nucleoside inhibitor of HIV-1 reverse
transcriptase". International Journal of Quantum Chemistry 107 2 (2007): 292-298. http://www.scopus.com/inward/record.url?eid=2-s2.0-33845967151&partnerID=MN8TOARS.
10.1002/qua.21192
- Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Theoretical studies on farnesyltransferase: Evidence for thioether product coordination
to the active-site zinc sphere". Journal of Computational Chemistry 28 7 (2007): 1160-1168. http://www.scopus.com/inward/record.url?eid=2-s2.0-34247548408&partnerID=MN8TOARS.
10.1002/jcc.20577
- Moreira, I.S.; Fernandes, P.A.; Ramos, M.J.. "Backbone importance for protein-protein binding". Journal of Chemical Theory
and Computation 3 3 (2007): 885-893. http://www.scopus.com/inward/record.url?eid=2-s2.0-36148995097&partnerID=MN8TOARS.
10.1021/ct6003824
- Sousa Moreira, I.; Fernandes, P.A.; Ramos, M.J.. "Vascular endothelial growth factor (VEGF) inhibition - A critical review".
Anti-Cancer Agents in Medicinal Chemistry 7 2 (2007): 223-245. http://www.scopus.com/inward/record.url?eid=2-s2.0-33947123052&partnerID=MN8TOARS.
10.2174/187152007780058687
- Moreira, I.S.; Fernandes, P.A.; Ramos, M.J.. "Hot spot occlusion from bulk water: A comprehensive study of the complex between
the lysozyme HEL and the antibody FVD1.3". Journal of Physical Chemistry B 111 10 (2007): 2697-2706. http://www.scopus.com/inward/record.url?eid=2-s2.0-34047271259&partnerID=MN8TOARS.
10.1021/jp067096p
- Perez, M.A.S.; Fernandes, P.A.; Ramos, M.J.. "Drug design: New inhibitors for HIV-1 protease based on Nelfinavir as lead".
Journal of Molecular Graphics and Modelling 26 3 (2007): 634-642. http://www.scopus.com/inward/record.url?eid=2-s2.0-34848852204&partnerID=MN8TOARS.
10.1016/j.jmgm.2007.03.009
- Carvalho, A.T.P.; Fernandes, P.A.; Ramos, M.J.. "The excision mechanism in reverse transcriptase: Pyrophosphate leaving and
fingers opening are uncoupled events with the analogues AZT and d4T". Journal of Physical Chemistry B 111 41 (2007):
12032-12039. http://www.scopus.com/inward/record.url?eid=2-s2.0-35948998054&partnerID=MN8TOARS.
10.1021/jp0746594
- Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Comparative assessment of theoretical methods for the determination of geometrical
properties in biological zinc complexes". Journal of Physical Chemistry B 111 30 (2007): 9146-9152. http://www.scopus.com/inward/record.url?eid=2-s2.0-34548202669&partnerID=MN8TOARS.
10.1021/jp072538y
- Moreira, I.S.; Fernandes, P.A.; Ramos, M.J.. "Hot spots - A review of the protein-protein interface determinant amino-acid
residues". Proteins: Structure, Function and Genetics 68 4 (2007): 803-812. http://www.scopus.com/inward/record.url?eid=2-s2.0-34548779127&partnerID=MN8TOARS.
10.1002/prot.21396
- Tamames, B.; Sousa, S.F.; Tamames, J.; Fernandes, P.A.; Ramos, M.J.. "Analysis of zinc-ligand bond lengths in metalloproteins:
Trends and patterns". Proteins: Structure, Function and Genetics 69 3 (2007): 466-475. http://www.scopus.com/inward/record.url?eid=2-s2.0-35448995715&partnerID=MN8TOARS.
10.1002/prot.21536
- Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J.. "Understanding ribonucleotide reductase inactivation by gemcitabine".
Chemistry - A European Journal 13 30 (2007): 8507-8515. http://www.scopus.com/inward/record.url?eid=2-s2.0-35348969874&partnerID=MN8TOARS.
10.1002/chem.200700260
- Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "General performance of density functionals". Journal of Physical Chemistry
A 111 42 (2007): 10439-10452. http://www.scopus.com/inward/record.url?eid=2-s2.0-35748980308&partnerID=MN8TOARS.
10.1021/jp0734474
- Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J.. "Ribonucleotide reductase: A critical enzyme for cancer chemotherapy
and antiviral agents". Recent Patents on Anti-Cancer Drug Discovery 2 1 (2007): 11-29. http://www.scopus.com/inward/record.url?eid=2-s2.0-34248170858&partnerID=MN8TOARS.
10.2174/157489207779561408
- Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Effective tailor-made force field parameterization of the several Zn coordination
environments in the puzzling FTase enzyme: Opening the door to the full understanding of its elusive catalytic mechanism".
Theoretical Chemistry Accounts 117 1 (2007): 171-181. http://www.scopus.com/inward/record.url?eid=2-s2.0-33751235864&partnerID=MN8TOARS.
10.1007/s00214-006-0170-9
- Moreira, I.S.; Fernandes, P.A.; Ramos, M.J.. "Unravelling hot spots: A comprehensive computational mutagenesis study". Theoretical
Chemistry Accounts 117 1 (2007): 99-113. http://www.scopus.com/inward/record.url?eid=2-s2.0-33751248238&partnerID=MN8TOARS.
10.1007/s00214-006-0151-z
- Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Theoretical studies on farnesyltransferase: The distances paradox explained".
Proteins: Structure, Function and Genetics 66 1 (2007): 205-218. http://www.scopus.com/inward/record.url?eid=2-s2.0-33845671721&partnerID=MN8TOARS.
10.1002/prot.21219
- Moreira, I.S.; Fernandes, P.A.; Ramos, M.J.. "Detailed microscopic study of the full ZipA:FtsZ interface". Proteins: Structure,
Function and Genetics 63 4 (2006): 811-821. http://www.scopus.com/inward/record.url?eid=2-s2.0-33646784622&partnerID=MN8TOARS.
10.1002/prot.20944
- Moreira, I.S.; Fernandes, P.A.; Ramos, M.J.. "Unraveling the importance of protein-protein interaction: Application of a computational
alanine-scanning mutagenesis to the study of the IgG1 streptococcal protein G (C2 Fragment) complex". Journal of Physical
Chemistry B 110 22 (2006): 10962-10969. http://www.scopus.com/inward/record.url?eid=2-s2.0-33745467541&partnerID=MN8TOARS.
10.1021/jp054760d
- Carvalho, A.P.; Fernandes, P.A.; Ramos, M.J.. "Molecular insights into the mechanisms of HIV-1 reverse transcriptase resistance
to nucleoside analogs". Mini-Reviews in Medicinal Chemistry 6 5 (2006): 549-555. http://www.scopus.com/inward/record.url?eid=2-s2.0-33646590228&partnerID=MN8TOARS.
10.2174/138955706776876276
- Carvalho, A.T.P.; Fernandes, P.A.; Ramos, M.J.. "Determination of the ¿pKa between the active site cysteines of thioredoxin
and DsbA". Journal of Computational Chemistry 27 8 (2006): 966-975. http://www.scopus.com/inward/record.url?eid=2-s2.0-33646560034&partnerID=MN8TOARS.
10.1002/jcc.20404
- Marques, A.T.; Antunes, A.; Fernandes, P.A.; Ramos, M.J.. "Comparative evolutionary genomics of the HADH2 gene encoding Aß-binding
alcohol dehydrogenase/17ß-hydroxysteroid dehydrogenase type 10 (ABAD/HSD10)". BMC Genomics 7 (2006): http://www.scopus.com/inward/record.url?eid=2-s2.0-33748344899&partnerID=MN8TOARS.
10.1186/1471-2164-7-202
- Branco, R.J.F.; Fernandes, P.A.; Ramos, M.J.. "Molecular dynamics simulations of the enzyme Cu, Zn superoxide dismutase".
Journal of Physical Chemistry B 110 33 (2006): 16754-16762. http://www.scopus.com/inward/record.url?eid=2-s2.0-33748541278&partnerID=MN8TOARS.
10.1021/jp056855l
- Carvalho, A.P.; Fernandes, P.A.; Ramos, M.J.. "Similarities and differences in the thioredoxin superfamily". Progress in
Biophysics and Molecular Biology 91 3 (2006): 229-248. http://www.scopus.com/inward/record.url?eid=2-s2.0-33645115156&partnerID=MN8TOARS.
10.1016/j.pbiomolbio.2005.06.012
- Fernandes, P.A.; Araújo, M.L.A.C.; Barbosa, A.J.M.; Alves, C.N.; Ferreira, Z.Q.; Gonzalez, C.R.-N.; Lima, C.F.R.A.C.; et al.
"Lead optimisation: Improving the affinity of the antiretrovirals nelfinavir and amprenavir for HIV-1 protease". Letters
in Drug Design and Discovery 3 6 (2006): 383-389. http://www.scopus.com/inward/record.url?eid=2-s2.0-33746712231&partnerID=MN8TOARS.
10.2174/157018006777805576
- Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J.. "Enzyme ribonucleotide reductase: Unraveling an enigmatic paradigm of
enzyme inhibition by furanone derivatives". Journal of Physical Chemistry B 110 42 (2006): 21272-21281. http://www.scopus.com/inward/record.url?eid=2-s2.0-33751297639&partnerID=MN8TOARS.
10.1021/jp0608269
- Carvalho, A.T.P.; Fernandes, P.A.; Ramos, M.J.. "Insights on resistance to reverse transcriptase: The different patterns of
interaction of the nucleoside reverse transcriptase inhibitors in the deoxyribonucleotide triphosphate binding site relative
to the normal substrate". Journal of Medicinal Chemistry 49 26 (2006): 7675-7682. http://www.scopus.com/inward/record.url?eid=2-s2.0-33845958917&partnerID=MN8TOARS.
10.1021/jm060698c
- Carvalho, A.T.P.; Fernandes, P.A.; Ramos, M.J.. "Molecular dynamics model of unliganded HIV-1 reverse transcriptase". Medicinal
Chemistry 2 5 (2006): 491-498. http://www.scopus.com/inward/record.url?eid=2-s2.0-33748677715&partnerID=MN8TOARS.
10.2174/157340606778250270
- Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Protein-ligand docking: Current status and future challenges". Proteins: Structure,
Function and Genetics 65 1 (2006): 15-26. http://www.scopus.com/inward/record.url?eid=2-s2.0-33748276474&partnerID=MN8TOARS.
10.1002/prot.21082
- Pereira, S.; Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J.. "Computational studies on class I ribonucleotide reductase:
Understanding the mechanisms of action and inhibition of a cornerstone enzyme for the treatment of cancer". European Biophysics
Journal 35 2 (2006): 125-135. http://www.scopus.com/inward/record.url?eid=2-s2.0-29944434730&partnerID=MN8TOARS.
10.1007/s00249-005-0026-6
- Ramos, M.J.; Fernandes, P.A.. "Atomic-level rational drug design". Current Computer-Aided Drug Design 2 1 (2006): 57-81.
http://www.scopus.com/inward/record.url?eid=2-s2.0-33746206391&partnerID=MN8TOARS.
10.2174/157340906776056464
- Carvalho, A.T.P.; Fernandes, P.A.; Ramos, M.J.. "Theoretical study of the unusual protonation properties of the active site
cysteines in thioredoxin". Journal of Physical Chemistry B 110 11 (2006): 5758-5761. http://www.scopus.com/inward/record.url?eid=2-s2.0-33645676926&partnerID=MN8TOARS.
10.1021/jp053275f
- Branco, R.J.F.; Fernandes, P.A.; Ramos, M.J.. "Cu, Zn Superoxide dismutase: Distorted active site binds substrate without
significant energetic cost". Theoretical Chemistry Accounts 115 1 (2006): 27-31. http://www.scopus.com/inward/record.url?eid=2-s2.0-32444433270&partnerID=MN8TOARS.
10.1007/s00214-005-0672-x
- Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Eriksson, L.A.; Ramos, M.J.. "Dehydration of ribonucleotides catalyzed by ribonucleotide
reductase: The role of the enzyme". Biophysical Journal 90 6 (2006): 2109-2119. http://www.scopus.com/inward/record.url?eid=2-s2.0-33645979395&partnerID=MN8TOARS.
10.1529/biophysj.104.054627
- Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Unraveling the mechanism of the farnesyltransferase enzyme". Journal of Biological
Inorganic Chemistry 10 1 (2005): 3-10. http://www.scopus.com/inward/record.url?eid=2-s2.0-12944324735&partnerID=MN8TOARS.
10.1007/s00775-004-0612-6
- Pereira, S.; Fernandes, P.A.; Ramos, M.J.. "Theoretical study on the inhibition of ribonucleotide reductase by 2'-mercapto-2'-deoxyribonucleoside-5'-diphosphates".
Journal of the American Chemical Society 127 14 (2005): 5174-5179. http://www.scopus.com/inward/record.url?eid=2-s2.0-17144411095&partnerID=MN8TOARS.
10.1021/ja046662w
- Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Farnesyltransferase - New insights into the zinc-coordination sphere paradigm:
Evidence for a carboxylate-shift mechanism". Biophysical Journal 88 1 (2005): 483-494. http://www.scopus.com/inward/record.url?eid=2-s2.0-11244321501&partnerID=MN8TOARS.
10.1529/biophysj.104.048207
- Ramos, M.J.; Fernandes, P.A.. "Computer modeling and research in the classroom". Journal of Chemical Education 82 7
(2005): 1021-1025. http://www.scopus.com/inward/record.url?eid=2-s2.0-21244459676&partnerID=MN8TOARS.
- Moreira, I.S.; Fernandes, P.A.; Ramos, M.J.. "Accuracy of the numerical solution of the Poisson-Boltzmann equation". Journal
of Molecular Structure: THEOCHEM 729 1-2 SPEC. (2005): 11-18. http://www.scopus.com/inward/record.url?eid=2-s2.0-24344502228&partnerID=MN8TOARS.
10.1016/j.theochem.2004.12.049
- Fernandes, P.A.; Henriques, E.S.; Pande, V.; Ramos, M.J.; Maia, A.R.R.; Almeida, A.A.S.; Silva, B.F.B.; et al. "New designs
for inhibitors of the NF-¿B: DNA binding". Theoretical Chemistry Accounts 113 4 (2005): 197-204. http://www.scopus.com/inward/record.url?eid=2-s2.0-21044448195&partnerID=MN8TOARS.
10.1007/s00214-005-0628-1
- Cerqueira, N.M.F.S.A.; Pereira, S.; Fernandes, P.A.; Ramos, M.J.. "Overview of ribonucleotide reductase inhibitors: An appealing
target in anti-tumour therapy". Current Medicinal Chemistry 12 11 (2005): 1283-1294. http://www.scopus.com/inward/record.url?eid=2-s2.0-19044394312&partnerID=MN8TOARS.
10.2174/0929867054020981
- Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. "Farnesyltransferase: Theoretical studies on peptide substrate entrance - Thiol
or thiolate coordination?". Journal of Molecular Structure: THEOCHEM 729 1-2 SPEC. (2005): 125-129. http://www.scopus.com/inward/record.url?eid=2-s2.0-24344434552&partnerID=MN8TOARS.
10.1016/j.theochem.2005.03.022
- Branco, R.J.F.; Fernandes, P.A.; Ramos, M.J.. "Density-functional calculations of the Cu, Zn superoxide dismutase redox potential:
The influence of active site distortion". Journal of Molecular Structure: THEOCHEM 729 1-2 SPEC. (2005): 141-146. http://www.scopus.com/inward/record.url?eid=2-s2.0-24344466892&partnerID=MN8TOARS.
10.1016/j.theochem.2004.12.046
- Ramos, M.J.; Magalhães, A.L.; Melo, A.S.; Fernandes, P.A.. "Foreword". Journal of Molecular Structure: THEOCHEM 729
1-2 SPEC. (2005): http://www.scopus.com/inward/record.url?eid=2-s2.0-24344432007&partnerID=MN8TOARS.
10.1016/j.theochem.2005.04.028
- Ramos, M. J.; Fernandes, P. A.; Melo, A.; Ramos, M.J.; Fernandes, P.A.. "Modeling chemical and biological systems: A successful
course for undergraduate students". Journal of Chemical Education 81 1 (2004): 72-75. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000187308400030&KeyUID=WOS:000187308400030.
10.1021/ed081p72
- Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Eriksson, L.A.; Ramos, M.J.. "Ribonucleotide activation by enzyme Ribonucleotide Reductase:
Understanding the role of the enzyme". Journal of Computational Chemistry 25 16 (2004): 2031-2037. http://www.scopus.com/inward/record.url?eid=2-s2.0-9244264943&partnerID=MN8TOARS.
10.1002/jcc.20127
- Fernandes, P.A.; Ramos, M.J.. "Theoretical Insights into the Mechanism for Thiol/Disulfide Exchange". Chemistry - A European
Journal 10 1 (2004): 257-266. http://www.scopus.com/inward/record.url?eid=2-s2.0-0347719283&partnerID=MN8TOARS.
10.1002/chem.200305343
- Fernandes, P.A.; Cruz, A.I.S.; Maia, A.R.R.; Almeida, A.A.S.; Da Silva, A.M.N.; Silva, B.F.B.; Ribeiro, C.M.S.; et al. "Design
of 2-cyclopentenone derivatives with enhanced NF-¿B: DNA binding inhibitory properties". Journal of Molecular Structure:
THEOCHEM 685 1-3 (2004): 73-82. http://www.scopus.com/inward/record.url?eid=2-s2.0-6944250787&partnerID=MN8TOARS.
10.1016/j.theochem.2004.06.027
- Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Eriksson, L.A.; Ramos, M.J.. "New insights into a critical biological control step
of the mechanism of Ribonucleotide reductase". Journal of Molecular Structure: THEOCHEM 709 1-3 SPEC. (2004): 53-65.
http://www.scopus.com/inward/record.url?eid=2-s2.0-11144306568&partnerID=MN8TOARS.
10.1016/j.theochem.2003.10.073
- Pereira, S.; Fernandes, P.A.; Ramos, M.J.. "Theoretical Study of Ribonucleotide Reductase Mechanism-Based Inhibition by 2'-Azido-2'-Deoxyribonucleoside
5'-Diphosphates". Journal of Computational Chemistry 25 2 (2004): 227-237. http://www.scopus.com/inward/record.url?eid=2-s2.0-0345763175&partnerID=MN8TOARS.
10.1002/jcc.10375
- Pereira, S.; Fernandes, P.A.; Ramos, M.J.. "Mechanism for ribonucleotide reductase inactivation by the anticancer drug gemcitabine".
Journal of Computational Chemistry 25 10 (2004): 1286-1294. http://www.scopus.com/inward/record.url?eid=2-s2.0-3042547835&partnerID=MN8TOARS.
10.1002/jcc.20054
- Lucas, M. D.; Fernandes, P. A.; Eriksson, L. A.; Ramos, M. J.. "Pyruvate formate lyase: A new perspective". Journal of
Physical Chemistry B 107 24 (2003): 5751-5757. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000183592000013&KeyUID=WOS:000183592000013.
10.1021/jp0223096
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al. "New designs for MRI contrast agents". Journal of Computer-Aided Molecular Design 17 7 (2003): 463-473. http://www.scopus.com/inward/record.url?eid=2-s2.0-0344271775&partnerID=MN8TOARS.
10.1023/A:1027347527385
- Fernandes, P.A.; Ramos, M.J.. "Theoretical studies on the mechanism of inhibition of ribonucleotide reductase by (E)-2'-fluoromethylene-2'-deoxycitidine-5'-diphosphate".
Journal of the American Chemical Society 125 20 (2003): 6311-6322. http://www.scopus.com/inward/record.url?eid=2-s2.0-0037950581&partnerID=MN8TOARS.
10.1021/ja0208613
- Silva, P.J.; Fernandes, P.A.; Ramos, M.J.. "A theoretical study of radical-only and combined radical/carbocationic mechanisms
of arachidonic acid cyclooxygenation by prostaglandin H synthase". Theoretical Chemistry Accounts 110 5 (2003): 345-351.
http://www.scopus.com/inward/record.url?eid=2-s2.0-0347592865&partnerID=MN8TOARS.
10.1007/s00214-003-0476-9
- Fernandes, P.A.; Ramos, M.J.. "Theoretical Studies on the Mode of Inhibition of Ribonucleotide Reductase by 2'-Substituted
Substrate Analogues". Chemistry - A European Journal 9 23 (2003): 5916-5925. http://www.scopus.com/inward/record.url?eid=2-s2.0-0347228946&partnerID=MN8TOARS.
10.1002/chem.200304948
- Fernandes, P.A.; Eriksson, L.A.; Ramos, M.J.. "The reduction of ribonucleotides catalyzed by the enzyme ribonucleotide reductase".
Theoretical Chemistry Accounts 108 6 (2002): 352-364. http://www.scopus.com/inward/record.url?eid=2-s2.0-0036976685&partnerID=MN8TOARS.
10.1007/s00214-002-0393-3
- Fernandes, P. A.; Cordeiro, Mnds; Gomes, Janf. "Molecular simulation of the interface between two immiscible electrolyte solutions".
Journal of Physical Chemistry B 105 5 (2001): 981-993. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000166846100011&KeyUID=WOS:000166846100011.
10.1021/jp002571j
- Gomes, Janf; Fernandes, P. A.; Natalia, M.; Cordeiro, D. S.. "Simulation of liquid/liquid interfaces and ion transfer". Abstracts
of Papers of the American Chemical Society 220 (2000): U232-U232. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000166091201182&KeyUID=WOS:000166091201182.
- Fernandes, P.A.; Natália, M.; Cordeiro, D.S.; Gomes, J.A.N.F.. "Influence of Ion Size and Charge in Ion Transfer Processes
Across a Liquid|Liquid Interface". Journal of Physical Chemistry B 104 10 (2000): 2278-2286. http://www.scopus.com/inward/record.url?eid=2-s2.0-0001606789&partnerID=MN8TOARS.
10.1021/jp993045z
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interface". Journal of Physical Chemistry B 103 30 (1999): 6290-6299. http://www.scopus.com/inward/record.url?eid=2-s2.0-0000578941&partnerID=MN8TOARS.
10.1021/jp9844213
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with water". Journal of Physical Chemistry B 103 7 (1999): 1176-1184. http://www.scopus.com/inward/record.url?eid=2-s2.0-0344004660&partnerID=MN8TOARS.
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of the water/1,2-dichloroethane interface". Journal of Molecular Structure: THEOCHEM 463 1-2 (1999): 151-156. http://www.scopus.com/inward/record.url?eid=2-s2.0-0033597061&partnerID=MN8TOARS.
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