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-- In 2003, I completed a Ph.D. in BioOrganic Chemistry at the Univ. of Bern, CH. In the following 6 years, as a pos-doc at ITQB-­UNL, I completely changed my scientific path to a new field, towards molecular modelling and simulation. In 2009, I was awarded my first FCT-funded contract as an independent researcher at the Faculty of Sciences, Univ. of Lisbon (FCUL), and the Machuqueiro Lab (http://mms.rd.ciencias.ulisboa.pt) was born. Since then, I have consolidated my scientific independence and transitioned to a group leader status, supported by the funding obtained over the years and the collaboration of many bright young students who have since joined the group. -- During my research career, I have authored and co-authored 96 papers/book chapters in high-impact peer-­reviewed international journals, an h-index of 32 (in G.Scholar), and a total number of citations of ~3200, giving an average of ~33 citations per paper. I also supervised 5 postdoc researchers, 14 Ph.D. theses (4 completed & 10 ongoing), and 19 MSc theses. I have secured 4 FCT-funded projects as a PI (PTDC/QUI­BIQ/113721/2009: €150k; PTDC/QEQ­COM/5904/2014: €185k; 2021.09635.CPCA: €12k; and 2022.15878.CPCA: €10k), 5 as co-PI/Team member (total: €666k; ~100k for my group), which supported the creation of a competitive computational infrastructure (the BioISI cluster with ~2500 cores & ~40 GPU units), which I manage and is currently being shared with several groups of my research unit (BioISI). -- My work on the development of constant­-pH MD methodologies applied to the water/membrane interface has become internationally recognized in the area of biomolecular electrostatics. This internationalization is clearly illustrated by the invitation to become editor of PlosOne, JCBC, and JMBi, and to review papers in very prestigious journals like JACS, JCTC, JCIM, Nature Sci. Rep., Biochemistry, JPhysChemLett, JPhysChemB, PlosOne, etc. I have also been invited to give talks at several expert meetings in the USA (''Proton Transfer in Biology'', 2010, CO; ''ACS Fall Meeting'', 2013, Indianapolis, IN; and the ''Protein Electrostatics'' (PE) in 2017, 2019, and 2022, Telluride, CO), and in Europe (''PE'' meetings, 2014, Lisbon, PT; 2016, Berlin, DE; 2018, Belgrade, SR; 2021, Genova, IT, ''webinar''), and 2023, Genova, IT. In addition, I have ~30 other invited oral presentations in national and international venues. I have also organized the international ''Protein Electrostatics'' meeting where the most influential researchers in this field gathered in Lisbon. I represented Portugal in the management committee of two COST Actions, CM1102 ''MultiGlycoNano'' and CA21162 "COZYME", which just started. I am also a member of 2 other ongoing COST Actions (CA18113 and CA21164). I was involved in an NIH grant approval (R01GM073857) in collaboration with Prof. Don Engelman (Yale) and I am also a member of the local cluster at FC.ID/ULisboa for HORIZON-WIDERA-2021-ACCESS-03, Project ID: 101079147 "Twinning for excellence in biophysics of protein interactions and self-assembly (TWIN2PIPSA)". I have a long tradition of participating in presentations for university students, intended to give an overview of the biomolecular modeling scientific area. Concerning the general public, I regularly participate in school presentations, public exhibitions, and other events.
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Identification

Personal identification

Full name
Miguel Machuqueiro

Citation names

  • Machuqueiro, Miguel

Author identifiers

Ciência ID
D416-CB5B-AC3D
ORCID iD
0000-0001-6923-8744
Google Scholar ID
vMBlK7AAAAAJ
Researcher Id
C-8012-2011
Scopus Author Id
57221975472

Email addresses

  • machuque@ciencias.ulisboa.pt (Professional)

Telephones

Telephone
  • 217500112 (Professional)

Addresses

  • Faculdade de Ciências da Universidade de Lisboa. Campo Grande, Edifício C8 (sala 8.5.52), 1749-016, Lisboa, Lisboa, Portugal (Professional)

Websites

Knowledge fields

  • Natural sciences - Biological Sciences - Biochemistry

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
French Beginner (A1) Intermediate (B1) Beginner (A1) Beginner (A1)
Spanish; Castilian Intermediate (B1) Intermediate (B1) Beginner (A1) Intermediate (B1)
Italian Beginner (A1) Intermediate (B1) Beginner (A1) Beginner (A1)
German Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1)
Education
Degree Classification
2003/04/24
Concluded
 Doutoramento em Química Bioorgânica (Doutoramento)
Universidade de Berna, Switzerland
"Chemical Models of Zinc-dependent Enzymes: Methyltransferases and Class II Aldolases" (THESIS/DISSERTATION)
 5 (0-6)
1998/06/30
Concluded
 Bioquímica (Licenciatura)
Universidade de Lisboa Faculdade de Ciências, Portugal
"Simulação do Ciclo de Oxidação e Redução das Ubiquinonas num Modelo de Transporte Electrónico - Aplicação ao Peroxissoma" (THESIS/DISSERTATION)
 15 (0-20)
Affiliation

Teaching in Higher Education

Category
Host institution 		Employer
2024/12/18 - Current Assistant Professor (University Teacher) Universidade de Lisboa Faculdade de Ciências, Portugal
Universidade de Lisboa Faculdade de Ciências, Portugal
(...)
2014/06/15 - 2019/04/30 Invited Assistant Professor (University Teacher) Universidade de Lisboa Faculdade de Ciências, Portugal

Others

Category
Host institution 		Employer
2019/05/01 - 2024/12/17 Investigador Auxiliar (CEEC-IND 2017) Universidade de Lisboa Faculdade de Ciências, Portugal
Universidade de Lisboa Faculdade de Ciências, Portugal
(...)
2009/06/15 - 2014/06/14 Investigador Auxiliar (Ciência 2008) Universidade de Lisboa Faculdade de Ciências, Portugal
Universidade de Lisboa Faculdade de Ciências, Portugal
2006/09/16 - 2009/06/14 Pós-Doutoramento (2º triénio) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2003/09/01 - 2006/09/15 Pós-Doutoramento (1º triénio) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
1999/04/09 - 2003/04/24 Doutoramento em Química Bioorgânica Universidade de Berna, Switzerland
Universidade de Berna, Switzerland
1996/10/01 - 1998/06/30 Estágio de Licenciatura em Bioquímica (FCUL) Instituto Rocha Cabral, Portugal
Instituto Rocha Cabral, Portugal
Projects

Grant

Designation Funders
2022/03/01 - 2023/02/28 A fast deep learning approach to improve protein pKa predictions
2021.09635.CPCA
Principal investigator
Fundação para a Ciência e a Tecnologia, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2019/07/09 - 2021/04/09 As bases física da doença: O caso da Amiloidose Relacionada com a Diálise Physical Basis of Disease: The case of Dialysis Related Amyloidosis
PTDC/FIS-OUT/28210/2017
Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2001/04/01 - 2003/03/31 Model Studies of Zn-dependent Methyltransferases
63802
PhD Student Fellow
Schweizerischer Nationalfonds zur Förderung der wissenschaftlichen Forschung
Concluded
1999/04/01 - 2001/03/31 Model Studies of Zn-dependent Methyltransferases
54130
PhD Student Fellow
Schweizerischer Nationalfonds zur Förderung der wissenschaftlichen Forschung
Concluded

Contract

Designation Funders
2019/09 - Current Understanding and exploiting the impacts of low pH on micro-organisms - EuroMicropH
CMST COST Action CA18113
Researcher
European Commission
Ongoing
2019 - Current Physical Basis of Disease: The case of Dialysis Related Amyloidosis
PTDC/FIS-OUT/28210/2017
Researcher
Fundação para a Ciência e a Tecnologia
Ongoing
2019 - Current Uncovering blind spots in halogen bonding applications
PTDC/QUI-QFI/28455/2017
Researcher
Fundação para a Ciência e a Tecnologia
Ongoing
2019 - Current Deal with PAINS: strategies to identify membrane modulators
PTDC/BIA-BFS/28419/2017
Researcher
Fundação para a Ciência e a Tecnologia
Ongoing
2019 - Current Targeting multi-resistant tuberculosis with new potent isoniazid derivatives: an integrated medicinal chemistry approach
PTDC/MED-QUI/29036/2017
Researcher
Fundação para a Ciência e a Tecnologia
Ongoing
2018/09 - Current EUropean TOPology Interdisciplinary Action - Eutopia
CMST COST Action CA17139
Researcher
European Commission
Ongoing
2018/09 - Current New diagnostic and therapeutic tools against multidrug resistant tumors - Stratagem
CMST COST Action CM17104
Researcher
European Commission
Ongoing
2019/05/01 - 2025/04/30 Adding pH effects to improve computer-aided drug design
CEECIND/02300/2017/CP1387/CT0031
10.54499/CEECIND/02300/2017/CP1387/CT0031
Principal investigator
Universidade de Lisboa Faculdade de Ciências, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2023/05/01 - 2024/04/30 In silico study of peptidic dendrimers as transfection agents in RNA vaccines
2022.15878.CPCA
Principal investigator
Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2021/03/01 - 2024/02/29 Fármacos de ruténio-péptido: flechas para alvejar seletivamente o cancro da mama
PTDC/QUI-QIN/0146/2020
Researcher
Universidade de Lisboa Centro de Química Estrutural, Portugal

Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal

Associação para a Inovação e Desenvolvimento da FCT, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2021/01/15 - 2021/06/15 Deal with PAINS: strategies to spot membrane modulators
PTDC/BIA-BFS/28419/2017
 Fundação para a Ciência e a Tecnologia
Ongoing
2019/01/01 - 2019/12/31 Centro de Química e Bioquímica
UID/Multi/00612/2019
FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2019/01/01 - 2019/12/31 Instituto de Biosistemas & Ciências Integrativas
UID/Multi/04046/2019
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal

Universidade do Minho, Portugal

Universidade do Porto Faculdade de Ciências, Portugal

Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal

FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal

Universidade de Lisboa Faculdade de Ciências, Portugal

Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2016/04/01 - 2019/09/30 CpHMD-L simulations of pHLIP peptides: design of new tumor-targeted drug delivery systems
Provided by PTCRIS: 144544
Principal investigator
Fundação para a Ciência e a Tecnologia
2013/07 - 2016/06 Increasing the realism of membrane modelling in constant-pH molecular dynamics methods: inclusion of electrochemical gradients and lipid titration
Provided by PTCRIS: 126847
126847
Researcher
Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2011/01/01 - 2014/06/30 Adding realism to the molecular modeling of lipidic membranes: inclusion of pH effects
113721
Provided by PTCRIS: 113721
Principal investigator
Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2010/01 - 2013/06 Understanding structure-activity relationships in peptide dendrimers using a molecular modelling approach
Provided by PTCRIS: 100416
100416
Researcher
Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2010/01 - 2013/06 Including protonation effects in the simulation of peptides and proteins in membrane environments
Provided by PTCRIS: 104378
104378
Researcher
Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2010/01 - 2013/03 Study of pH-dependent protein misfolding using state-of-the-art molecular modeling methods
105238
Provided by PTCRIS: 105238
Researcher
Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2011/01/01 - 2012/12/31 Strategic Project - UI 612 - 2011-2012
PEst-OE/QUI/UI0612/2011
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2006/10/15 - 2009/06/14 MEMBRANE-INDUCED STRUCTURAL CHANGES IN PROTEINS: A COMPUTER SIMULATION STUDY
SFRH/BPD/29358/2006
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2003/10/01 - 2006/09/30 EFEITO DO pH E DA OXI-REDUÇÃO NA ESTRUTURA E DINÂMICA DE BIOMOLÉCULAS: ESTUDOS DE MODELAÇÃO MOLECULAR
SFRH/BPD/14540/2003
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded

Other

Designation Funders
2018 - 2021 TARGTUB - Targeting multi-resistant tuberculosis with new potent isoniazid derivatives: an integrated medicinal chemistry approach.
PTDC/MEDQUI/29036/2017
 Fundação para a Ciência e a Tecnologia
Ongoing
Outputs

Publications

Book
  1. Moreira, Irina S; Machuqueiro, Miguel; Mourão, Joana. Computational Design of Membrane Proteins. 2021.
    In press
Book chapter
  1. Salete J. Baptista; Beatriz Bueschbell; Pedro R. Magalhães; António J. Preto; Agostinho Lemos; Nícia Rosário-Ferreira; Anke C. Schiedel; et al. Corresponding author: Moreira, Irina S.. "Arrestin and G Protein Interactions with GPCRs: A Structural Perspective". In GPCRs as Therapeutic Targets, edited by Annette Gilchrist. United States: John Wiley & Sons, Inc., 2022.
    Published • 10.1002/9781119564782.ch5
  2. Magalhães, Pedro R.; Reis, Pedro B. P. S.; Vila-Viçosa, Diogo; Machuqueiro, Miguel; Victor, Bruno L.. Corresponding author: Victor, Bruno L.. "Identification of Pan-Assay INterference compoundS (PAINS) Using an MD-Based Protocol". In Computational Design of Membrane Proteins, edited by Miguel Machuqueiro; Irina S. Moreira; Joana B. Mourão, 263-271. Springer US, 2021.
    Published • 10.1007/978-1-0716-1468-6_15
  3. Oliveira, Nuno F. B.; Silva, Tomás F. D.; Reis, Pedro B. P. S.; Machuqueiro, Miguel. Corresponding author: Machuqueiro, Miguel. "pKa Calculations in Membrane Proteins from Molecular Dynamics Simulations". In Computational Design of Membrane Proteins, edited by Miguel Machuqueiro; Irina S. Moreira; Joana B. Mourão, 185-195. United States: Springer US, 2021.
    Published • 10.1007/978-1-0716-1468-6_11
Conference abstract
  1. Silva, Tomás F.D.; Vila-Viçosa, Diogo; Machuqueiro, Miguel. "Tackling the realism: A pH gradient approach to transmembrane peptides¿ simulations". Paper presented in 2022 3D-BioInfo-PT Meeting, Oeiras, 2022.
  2. João G. N. Sequeira; Link, Wolfgang; Machuqueiro, Miguel. Corresponding author: João G. N. Sequeira. "HTVS protocol to identify non-covalent inhibitors of CRM1". Paper presented in Encontro de Jovens Investigadores de Biologia Computacional Estrutural, Coimbra, 2021.
    10.3390/mol2net-07-12108
  3. João G. N. Sequeira; Filipe E. P. Rodrigues; Telmo G. D. Silva; Pedro B. P. S. Reis; Machuqueiro, Miguel. Corresponding author: Machuqueiro, Miguel. "Extension of the stochastic CpHMD method to the CHARMM36m force field". Paper presented in Encontro de Jovens Investigadores de Biologia Computacional Estrutural, Coimbra, 2021.
    10.3390/mol2net-07-12117
  4. Nunes, Rafael; Vila-Vicosa, Diogo; Machuqueiro, Miguel; Costa, Paulo J.. "Improved modeling of halogen-protein interactions in biomolecular simulations using a GROMOS force field". Paper presented in JOINT 12th EBSA congress and 10th ICBP ¿ IUPAP congress, Madrid, 2019.
    Published • 10.1007/s00249-019-01373-4
  5. Oliveira, Nuno; Pires, Inês; Machuqueiro, Miguel. "New phosphorylated amino acid parametrization to correctly reproduce their acid/base equilibria, including in protein binding events". Paper presented in EJIBCE-02: Meeting of Young Researchers in Structural Computational Biology, Porto, 2018.
    10.3390/mol2net-04-06082
  6. Silva, Tomás; Vila-Viçosa, Diogo; Reshetnyak, Yana; Andreev, Oleg; Machuqueiro, Miguel. "In silico studies on the pH induced membrane insertion of pHLIP peptides". Paper presented in EJIBCE 2017, Coimbra, 2017.
    10.3390/mol2net-03-05079
  7. Nunes, Rafael; Costa, Paulo J.; Vila-Viçosa, Diogo; Machuqueiro, Miguel. "T4 Lysozyme/Halobenzene: A Test System for Modeling Biomolecular Halogen Bonds". Paper presented in MOL2NET 2017, International Conference on Multidisciplinary Sciences, 3rd edition, Sciforum Electronic Conference Series, 2017.
    Published • 10.3390/mol2net-03-05075
Conference paper
  1. Barreto, Carlos; Machuqueiro, Miguel; Bonvin, Alexandre; Moreira, Irina. "Structural and dynamic understanding of the ghrelin receptor high constitutive activity". Paper presented in MOL2NET 2017, 2017.
    10.3390/mol2net-03-05089
Conference poster
  1. Pires, I.D.S.; Baptista, António M.; Machuqueiro, Miguel. Corresponding author: Pires, I.D.S.. "Studying Cytochrome c Oxidase proton pumping mechanism with Constant-pH simulations". Paper presented in 4th Biophysics Festival, 2024.
  2. Sequeira, João G. N.; Roitberg, Adrian; Machuqueiro, Miguel. "Extending the Stochastic titration CpHMD Method to AMBER14SB for Acid-Sensing Ion Channels Modeling". Paper presented in Hünfeld 2024: Workshop on Computer Simulation and Theory of Macromolecules, 2024.
  3. Pires, I.D.S.; Morais, Tânia S.; Machuqueiro, Miguel. "In silico study of promising ruthenium metalodrug delivery systems". Paper presented in 3rd Chem & Biochem Students Meeting, FCUL, Lisboa, Portugal, 2023.
  4. Sequeira, João G. N.; Roitberg, Adrian; Machuqueiro, Miguel. Corresponding author: Sequeira, João G. N.. "The role of pH in the search for non-opioid analgesics: What we are doing about it and why". Paper presented in 3rd Chem & BioChem Students Meeting, 2023.
  5. Inês Silva Pires; Morais, Tânia S.; Machuqueiro, Miguel. "In silico study of promising ruthenium metallodrug delivery systems". Paper presented in 3rd Chem&Biochem, 2023.
  6. Pires, I.D.S.; Machuqueiro, Miguel. "How protein pKa predictions are affected by the choice of experimental structure?". Paper presented in Protein Electrostatics 2023, Genoa, IT., 2023.
  7. Suzano, Pedro; Silva, Tomas F. D.; Pires, Ines D. S.; Oliveira, Nuno F. B.; Reis, Pedro; Machuqueiro, Miguel. "MembIT - a Powerful Tool for Analyzing Solute Membrane Insertions and Deformations in MD Simulations". Paper presented in Protein Electrostatics Conference, 2023.
  8. Pires, I.D.S.; Morais, Tânia S.; Machuqueiro, Miguel. "Evaluating the membrane biophysical profile of smart metallodrugs for cancer therapy". Paper presented in Virtual Winter School on Computational Chemistry, Online Workshop, 2023.
  9. Silva, Tomás F.D.; Suzano, Pedro; Pires, I.D.S.; Oliveira, Nuno F. B.; Reis, Pedro B P S; Machuqueiro, Miguel. Corresponding author: Suzano, Pedro. "MembIT - a tool to calculate membrane-insertion properties of solutes". Paper presented in 3D-BIOINFO-PT Annual Meeting, 2022.
  10. Pires, I.D.S.; Morais, Tânia S.; Machuqueiro, Miguel. "Computational biophysics evaluation of promising smart metallodrug delivery system". Paper presented in 3D-BIOINFO-PT Annual Meeting, 2022.
  11. Sequeira, João G. N.; Link, Wolfgang; Machuqueiro, Miguel. Corresponding author: Sequeira, João G. N.. "Searching for CRM1 inhibitors using a HTVS protocol". Paper presented in 3D-BioInfo-PT annual meeting, 2022.
  12. Vitorino, João N. M.; Oliveira, Nuno; Filipe E. P. Rodrigues; Faísca, Patrícia FN; Machuqueiro, Miguel. "Predicting Aggregation-Triggering ¿2m Oligomers With The Help Of MMPBSA Calculations". Paper presented in 3D-BIOINFO-PT Annual Meeting, 2022.
  13. Oliveira, N. F. B.; Yousef, Mohannad; Machuqueiro, Miguel. "Computational estimation of protein/drug pH-dependent binding affinities". Paper presented in 3D-BIOINFO-PT Annual Meeting, 2022.
  14. Sequeira, João G. N.; Link, Wolfgang; Machuqueiro, Miguel. Corresponding author: Sequeira, João G. N.. "High-throughput virtual screening to identify non-covalent inhibitors of CRM1 with anti-tumoral potential". Paper presented in 6ª Conferência Anual da RedeSAÚDE, 2022.
  15. Suzano, Pedro; Silva, Tomás F.D.; Machuqueiro, Miguel. Corresponding author: Suzano, Pedro. "A Computational Method to Estimate pH Effects in Antitumor Drug Resistance". Paper presented in 2nd Chem & Biochem Students Meeting, 2022.
  16. Sequeira, João G. N.; Link, Wolfgang; Machuqueiro, Miguel. Corresponding author: Sequeira, João G. N.. "An ad hoc HTVS protocol to identify new CRM1 non-covalent inhibitors". Paper presented in 2nd Chem & BioChem Students Meeting, 2022.
  17. Ricardo G. Teixeira; Belisario, Dimas C.; Oliveira, Nuno F. B.; Sequeira, João G. N.; Romero, Isabel; Riganti, Chiara; Machuqueiro, Miguel; et al. Corresponding author: Valente, Andreia. "Targeting P-gp with Ru-cyclopentadienyl compounds: an approach to overcome cancer multidrug resistance". Paper presented in CQE Days, 2022.
  18. Tânia S. Morais; João Franco Machado; Sá, Marco; Machuqueiro, Miguel; Fernanda Marques; Helena Garcia, Maria; Correia, João D. G.. Corresponding author: Tânia S. Morais. "Targeted delivery of Ru-cyclopentadienyl complexes to breast cancer cells with FGFR-specific peptides". Paper presented in 8th Latin American Symposium on Coordination and Organometallic Chemistry (Virtual), 2022.
  19. Vitorino, João N. M.; Reis, Pedro B P S; Machuqueiro, Miguel. Corresponding author: Vitorino, João N. M.. "PyBindE: Development of a Simple Python MM-PBSA Implementation for Estimating Protein-Protein and Protein-Ligand Binding Energies". Paper presented in 9º Encontro de Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE 2021), 2021.
    mol2net-07-12107
  20. Magalhães, Pedro R.; Reis, Pedro B P S; Vila-Viçosa, Diogo; Machuqueiro, Miguel; Victor, Bruno. Corresponding author: Magalhães, Pedro R.. "Identification of membrane PAINS via an optimized computational protocol". Paper presented in 8th EJIBCE, Coimbra, Portugal, 2021.
  21. Silva, Tomás F.D.; Machuqueiro, Miguel. Corresponding author: Machuqueiro, Miguel. "Improved realism of peptide-membrane simulations using a pH-Gradient/CpHMD protocol". Paper presented in 8º Encontro Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE2021), 2021.
  22. Vitorino, João N. M.; Oliveira, N. F. B.; Rodrigues, F. E. P.; Machuqueiro, Miguel. Corresponding author: Vitorino, João N. M.. "Develop a Simple and Fast MM-PBSA Method Based on DelPhi to Study Protein/Protein Binding Affinities". Paper presented in Hünfeld 2021: Workshop on Computer Simulation and Theory of Macromolecules, 2021.
  23. Suzano, Pedro; Silva, Tomás F.D.; Machuqueiro, Miguel. Corresponding author: Suzano, Pedro. "In silico Study of Acid-Induced Anti-Tumor Drug Resistance". Paper presented in Computer Simulation and Theory of Macromolecules 2021, Online Workshop, 2021.
  24. Magalhães, Pedro R.; Reis, Pedro B P S; Vila-Viçosa, Diogo; Machuqueiro, Miguel; Victor, Bruno. Corresponding author: Magalhães, Pedro R.. "Development of a Novel Computational Protocol for the Identification of Membrane PAINS". Paper presented in Computer Simulation and Theory of Macromolecules, Hunfeld Online Workshop, 2021.
  25. Oliveira, N. F. B.; Machuqueiro, Miguel. "The Role of Electrostatics in the Mechanism of ATP/ADP Carrier Function: An in silico Study". Paper presented in Hünfeld 2021: Workshop on Computer Simulation and Theory of Macromolecules, 2021.
  26. Silva, Tomás F.D.; Vila-Viçosa, Diogo; Machuqueiro, Miguel. "Computational Methods to Tackle the pH Effects on Membrane-Inserting Peptides". Paper presented in Computer Simulation and Theory of Macromolecules 2021, Online Workshop, 2021.
  27. João G. N. Sequeira; Machuqueiro, Miguel. Corresponding author: João G. N. Sequeira. "Conformation characterization of the NES-binding groove in CRM1". Paper presented in Hünfeld 2021: Workshop on Computer Simulation and Theory of Macromolecules, 2021.
  28. Magalhães, Pedro R.; Reis, Pedro B P S; Vila-Viçosa, Diogo; Machuqueiro, Miguel; Victor, Bruno. "Speeding-up the identification of membrane PAINS with a new computational approach". Paper presented in Ciências Research Day, 2020.
  29. Magalhães, Pedro R.; Reis, Pedro B P S; Vila-Viçosa, Diogo; Machuqueiro, Miguel; Victor, Bruno. "Refining an umbrella-sampling protocol to describe membrane PAINS". Paper presented in EJIBCE 2019 (7th Encontro de Jovens Investigadores de Biologia Computacional Estrutural), Lisboa, Portugal, 2019.
  30. Magalhães, Pedro R.; Vila-Viçosa, Diogo; Machuqueiro, Miguel; Victor, Bruno. "Structural characterization of Aquaporin-1 and evaluation of a PMF based protocol to determine water permeability rates". Paper presented in EJIBCE 2019 (7th Encontro de Jovens Investigadores de Biologia Estrutural Compucacional), Lisboa, Portugal, 2019.
  31. Silva, Tomás F.D.; Machuqueiro, Miguel. "pH-dependent membrane crossing mechanism of lipophilic antitumoral drugs". Paper presented in EJIBCE 2019, 2019.
  32. Silva, Tomás F.D.; Vila-Viçosa, Diogo; Machuqueiro, Miguel. "Improving in silico membrane pKa calculations of pHLIP peptides,". Paper presented in EUROPIN Summer School on Drug Design, 2019.
  33. Magalhães, Pedro R.; Reis, Pedro B P S; Vila-Viçosa, Diogo; Machuqueiro, Miguel; Victor, Bruno. "Computational Characterization of Membrane PAINS". Paper presented in Joint 12th EBSA 10th ICBP-IUPAP Biophysics Congress, Madrid, Spain, 2019.
  34. Magalhães, Pedro R.; Vila-Viçosa, Diogo; Machuqueiro, Miguel; Victor, Bruno. "Computational prediction of water permeability rates in Aquaporin-1". Paper presented in Joint 12th EBSA congress 10th ICBP-IUPAP Congress, Madrid, Spain, 2019.
  35. Silva, Tomás F.D.; Vila-Viçosa, Diogo; Machuqueiro, Miguel. "pH Replica Exchange simulations of pHLIP peptides". Paper presented in 12th EBSA - IUPAP Biophysics Congress, 2019.
  36. Silva, Tomás F.D.; Vila-Viçosa, Diogo; Machuqueiro, Miguel. "Applying a pHRE method to pHLIP Peptides". Paper presented in BioISI PhD Symposium, 2019.
  37. Magalhães, Pedro R.; Reis, Pedro B P S; Vila-Viçosa, Diogo; Machuqueiro, Miguel; Victor, Bruno. "Optimization of a computational protocol to characterize membrane PAINS". Paper presented in Workshop on Integrative Approaches to Protein Folding & Aggregation, Lisboa, Portugal, 2019.
  38. Silva, Tomás F.D.; Vila-Viçosa, Diogo; Machuqueiro, Miguel. "A pH Replica Exchange approach to pHLIP peptides". Paper presented in Integrative Approaches to Protein Folding & Aggregation, 2019.
  39. Loureiro, Rui João; Vila-Viçosa, Diogo; Machuqueiro, Miguel; Shakhnovich, Eugene; Faísca, Patrícia. "The importance of unstructured termini in the aggregation cascade of beta-2-microglobulin: insights from molecular simulations of D76N mutant". Paper presented in EJIBCE 2018, 2018.
    10.3390/mol2net-04-06085
  40. Barreto, Carlos A.V.; Melo, Rita; Magalhães, Pedro R.; Renault, Pedro; Machuqueiro, Miguel; Moreira, Irina S.. "Understanding Structural and Dynamic Differences of GHSR-Gq nad GHSr-Arr Complexes". Paper presented in Encontro Jovens Investigadores de Biologia Estrutural e Computacional, 2018.
  41. Magalhães, Pedro R.; Vila-Viçosa, Diogo; Silva, Tomás; Machuqueiro, Miguel. "pH effects on PG/PC and PS/PC lipid binary mixtures: a CpHMD study". Paper presented in Protein Electrostatics Conference, Serbia, Belgrade, 2018.
  42. Silva, Tomás F.D.; Vila-Viçosa, Diogo; Slaybaugh, Gregory; Reshetnyak, Yana K.; Andreev, Oleg A.; Machuqueiro, Miguel. "Replica Exchange CpHMD simulations of pHLIP peptides". Paper presented in Protein Electrostatics, 2018.
  43. Vila-Viçosa, Diogo; Reis, Pedro B P S; Silva, Tomás F.D.; Machuqueiro, Miguel. "Coupling enhanced sampling and biased MD simulations with CpHMD". Paper presented in Protein Electrostatics, 2018.
  44. Magalhães, Pedro Rafael; Vila-Viçosa, Diogo; Silva, Tomás; Machuqueiro, Miguel. "pH effects on PG/PC and PS/PC lipid binary mixtures". Paper presented in Protein Electrostatics, 2018.
    10.3390/mol2net-04-05922
  45. Silva, Tomás F.D.; Reis, Pedro B P S; Victor, Bruno; Vila-Viçosa, Diogo; Machuqueiro, Miguel. "Evaluating GROMOS force fields without the twin-range cutoff scheme". Paper presented in Free Energy Calculations from Molecular Simulation: Aplications in Life and Medical Sciences, 2017.
  46. Nunes, Rafael; Pais, João; Vila-Vicosa, Diogo; Machuqueiro, Miguel; Rauter, Amélia P.. "Synthesis of new antibiotic glycosides and computational studies on their interaction with model lipid bilayers". Paper presented in CQB Day 2016, Lisboa, Portugal, 2016.
  47. Nunes, Rafael; Vila-Vicosa, Diogo; Rauter, Amélia P.; Machuqueiro, Miguel. "Sugar-based surfactants as antibacterial agents targeting lipid bilayers: Insights from molecular dynamics simulations". Paper presented in 3o Encontro de Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE 2015), Coimbra, Portugal, 2015.
  48. Nunes, Rafael; Pais, João; Vila-Vicosa, Diogo; Machuqueiro, Miguel; Rauter, Amélia P.. "Novel antibacterial glycosides: synthesis and computational studies on their interaction with model membranes". Paper presented in 11th International Meeting of the Portuguese Carbohydrate Group and 6th Iberian Carbohydrate Meeting, Viseu, Portugal, 2015.
  49. Nunes, Rafael; Pais, João; Vila-Vicosa, Diogo; Machuqueiro, Miguel; Rauter, Amélia P.. "New sugar-based surfactants targetting lipid bilayers: Synthesis and molecular dynamics study". Paper presented in CQB Day 2015, Lisboa, Portugal, 2015.
  50. Nunes, Rafael; Pais, João; Vila-Vicosa, Diogo; Machuqueiro, Miguel; Rauter, Amélia P.. "Synthesis and molecular dynamics study of new membrane-active antibacterial glycosides". Paper presented in 19th European Symposium on Organic Chemistry, Lisboa, Portugal, 2015.
  51. Nunes, Rafael; Vila-Vicosa, Diogo; Rauter, Amélia P.; Machuqueiro, Miguel. "New insights into the interaction of sugar-based surfactants with lipid bilayers from molecular dynamics simulations". Paper presented in 2o Encontro de Jovens Investigadores de Biologia Computacional Estrutural, Lisboa, Portugal, 2014.
  52. Nunes, Rafael; Vila-Vicosa, Diogo; Rauter, Amélia P.; Machuqueiro, Miguel. "A molecular view on the interaction of antibiotic deoxy glycosides with model phospholipid bilayers". Paper presented in MultyGlycoNano 2014 - COST Action CM1102 Meeting, Siena, Italy, 2014.
  53. Nunes, Rafael; Vila-Vicosa, Diogo; Rauter, Amélia P.; Machuqueiro, Miguel. "Interaction of antibacterial sugar-based surfactants with model lipid membranes: Insights from molecular dynamics simulations". Paper presented in Dynamic nano- and glyco-sciences, COST Action CM1102 spring training school, University of Namur, Belgium, 2014.
  54. Nunes, Rafael; Vila-Viçosa, Diogo; Rauter, Amélia P.; Machuqueiro, Miguel. "Molecular dynamics simulations of antimicrobial deoxy glycoside-based surfactants: Micellization and structural insights". Paper presented in 1o Encontro de Jovens Investigadores de Biologia Computacional Estrutural, Porto, Portugal, 2013.
  55. Magalhães, Pedro R.; Machuqueiro, Miguel; Baptista, António M.. "The effect of pH on the interaction between the neuropeptide kyotorphin and a lipid bilayer: a molecular simulation study". Paper presented in X Girona Seminar on Theoretical and Computational Chemistry for the Modeling of Biochemical Systems: From Theory to Applications, Girona, Spain, 2012.
  56. Baptista, António M.; Magalhães, Pedro R.; Campos, Sara R. R.; Machuqueiro, Miguel. "Ionization of a neuropeptide unaffected by the membrane environment: simulations of kyotorphin using constant-pH MD and linear response approximation". Paper presented in Gordon Research Conference on Protons & Membrane Reactions, San Francisco, USA, 2012.
  57. Magalhães, Pedro R.; Machuqueiro, Miguel; Baptista, António M.. "Simulation of explicit bilayers with constant-pH molecular dynamics". Paper presented in 5th Theoretical Biophysics International Symposium, Madeira, Portugal, 2011.
  58. Magalhães, Pedro R.; Machuqueiro, Miguel; Baptista, António M.. "Constant-pH molecular dynamics simulations of the neuropeptide kyotorphin in a lipid bilayer". Paper presented in Frontiers in Protein Research Interbio Symposium, Oeiras, Portugal, 2011.
  59. Magalhães, Pedro R.; Machuqueiro, Miguel; Baptista, António M.. "Constant-pH molecular dynamics simulations of explicit membranes: study of peptide-bilayer interactions". Paper presented in V Spanish-Portuguese Biophysics Congress, Zaragoza, Spain, 2010.
  60. Magalhães, Pedro R.; Machuqueiro, Miguel; Baptista, António M.. "Interaction between kyotorphin and biological membranes: a constant-pH MD study". Paper presented in Expanding the Frontiers of Molecular Dynamics Simulations in Biology Conference, Barcelona, Spain, 2009.
Journal article
  1. Nuno F.B. Oliveira; Alexey S. Ladokhin; Miguel Machuqueiro. Corresponding author: Miguel Machuqueiro. "Constant-pH MD simulations of the protonation-triggered conformational switching in diphtheria toxin translocation domain". Biophysical Journal 123 24 (2024): 4266-4273. https://doi.org/10.1016/j.bpj.2024.08.023.
    Published • 10.1016/j.bpj.2024.08.023
  2. Sara G. F. Ferreira; Manoj K. Sriramoju; Shang-Te Danny Hsu; Patrícia F. N. Faísca; Miguel Machuqueiro. Corresponding author: Miguel Machuqueiro. "Is There a Functional Role for the Knotted Topology in Protein UCH-L1?". Journal of Chemical Information and Modeling 64 17 (2024): 6827-6837. https://doi.org/10.1021/acs.jcim.4c00880.
    Published • 10.1021/acs.jcim.4c00880
  3. Carlos A. V. Barreto; João N. M. Vitorino; Pedro B.P.S. Reis; Miguel Machuqueiro; Irina S. Moreira. "pKa Calculations of GPCRs: Understanding Protonation States in Receptor Activation". Journal of Chemical Information and Modeling (2024): https://doi.org/10.1021/acs.jcim.4c01125.
    10.1021/acs.jcim.4c01125
  4. Filipe E. P. Rodrigues; Tamis Darbre; Miguel Machuqueiro. "High Charge Density in Peptide Dendrimers is Required to Destabilize Membranes: Insights into Endosome Evasion". Journal of Chemical Information and Modeling (2024): https://doi.org/10.1021/acs.jcim.4c00018.
    10.1021/acs.jcim.4c00018
  5. João Franco Machado; Marco Sá; Inês Pires; Miguel Tarita da Silva; Fernanda Marques; Jaime A. S. Coelho; Filipa Mendes; et al. "Dual FGFR-targeting and pH-activatable ruthenium–peptide conjugates for targeted therapy of breast cancer". Dalton Transactions (2024): https://doi.org/10.1039/D4DT00497C.
    10.1039/D4DT00497C
  6. Fortuna, Andreia; Suzano, Pedro M.S.; Machuqueiro, Miguel; Costa, Paulo J.. "Influence of Iodine Merz-Singh-Kollman Radius on the Calculated Charges and Hydration Free Energies of Iodinated Molecule". Journal of Computational Biophysics and Chemistry (2023): http://dx.doi.org/10.1142/s2737416523500722.
    Accepted • 10.1142/s2737416523500722
  7. Ricardo G. Teixeira; Iris C. Salaroglio; Nuno F. B. Oliveira; João G. N. Sequeira; Xavier Fontrodona; Isabel Romero; Miguel Machuqueiro; et al. "Fighting Multidrug Resistance with Ruthenium–Cyclopentadienyl Compounds: Unveiling the Mechanism of P-gp Inhibition". Journal of Medicinal Chemistry (2023): https://doi.org/10.1021/acs.jmedchem.3c01120.
    10.1021/acs.jmedchem.3c01120
  8. Tomás F. D. Silva; Hannah Visca; Craig Klumpp; Oleg A. Andreev; Yana K. Reshetnyak; Miguel Machuqueiro. "Arginine Residues Modulate the Membrane Interactions of pHLIP Peptides". Journal of Chemical Information and Modeling (2023): https://doi.org/10.1021/acs.jcim.3c00360.
    10.1021/acs.jcim.3c00360
  9. Rodnin, Mykola V.; Vasques-Montes, Victor; Kyrychenko, Alexander; Oliveira, Nuno F. B.; Kashipathy, Maithri M.; Battaile, Kevin P.; Douglas, Justin; et al. "Histidine Protonation and Conformational Switching in Diphtheria Toxin Translocation Domain". Toxins 15 7 (2023): 410. http://dx.doi.org/10.3390/toxins15070410.
    10.3390/toxins15070410
  10. Silva, Tomás F.D.; Visca, Hannah; Klumpp, Craig; Andreev, Oleg A.; Reshetnyak, Yana K.; Machuqueiro, Miguel. Corresponding author: Machuqueiro, Miguel. "Arginine Residues Modulate the Membrane Interactions of pHLIP Peptides". Journal of Chemical Information and Modeling (2023):
    Under revision
  11. Nuno F. B. Oliveira; Filipe E. P. Rodrigues; João N. M. Vitorino; Patrícia F. N. Faísca; Miguel Machuqueiro. "Interfacial Dynamics and Growth Modes of ß2-Microglobulin Dimers". Journal of Chemical Information and Modeling (2023): https://doi.org/10.1021/acs.jcim.3c00399.
    10.1021/acs.jcim.3c00399
  12. Pedro M. S. Suzano; Ines D. S. Pires; Tomas F. D. Silva; Nuno F. B. Oliveira; Pedro B. P. S. Reis; Miguel Machuqueiro. "MembIT - a tool to calculate solute membrane insertions and deformations in molecular dynamics simulations". Journal of Computational Biophysics and Chemistry (2023): https://doi.org/10.1142/S2737416523500254.
    10.1142/S2737416523500254
  13. Maria João Álvaro-Martins; Violeta Railean; Filomena Martins; Miguel Machuqueiro; Rita Pacheco; Susana Santos. "Synthesis and the In Vitro Evaluation of Antitumor Activity of Novel Thiobenzanilides". Molecules (2023): https://doi.org/10.3390/molecules28041877.
    10.3390/molecules28041877
  14. André M.M. Gomes; Paulo J. Costa; Miguel Machuqueiro. "Recent advances on molecular dynamics-based techniques to address drug membrane permeability with atomistic detail". BBA Advances (2023): https://doi.org/10.1016/j.bbadva.2023.100099.
    10.1016/j.bbadva.2023.100099
  15. Beatriz Bueschbell; Pedro R. Magalhães; Carlos A.V. Barreto; Rita Melo; Anke C. Schiedel; Miguel Machuqueiro; Irina S. Moreira. "The World of GPCR dimers – Mapping dopamine receptor D2 homodimers in different activation states and configuration arrangements". Computational and Structural Biotechnology Journal (2023): https://doi.org/10.1016/j.csbj.2023.08.032.
    10.1016/j.csbj.2023.08.032
  16. Lucia Jimenez; Victor Mayoral-Varo; Carlos Amenábar; Judit Ortega; João G. N. Sequeira; Miguel Machuqueiro; Cristiana Mourato; et al. "Multiplexed cellular profiling identifies an organoselenium compound as an inhibitor of CRM1 -mediated nuclear export". Traffic (2022): https://doi.org/10.1111/tra.12872.
    10.1111/tra.12872
  17. Tomás F. D. Silva; Diogo Vila-Viçosa; Miguel Machuqueiro. "Increasing the Realism of in Silico pHLIP Peptide Models with a Novel pH Gradient CpHMD Method". Journal of Chemical Theory and Computation (2022): https://doi.org/10.1021/acs.jctc.2c00880.
    10.1021/acs.jctc.2c00880
  18. Claudia Istrate; Jéssica Marques; Pedro Bule; Sílvia Correia; Frederico Aires-da-Silva; Marlene Duarte; Ana Luísa Reis; et al. "In Silico Characterization of African Swine Fever Virus Nucleoprotein p10 Interaction with DNA". Viruses (2022): https://doi.org/10.3390/v14112348.
    10.3390/v14112348
  19. João G. N. Sequeira; Filipe E. P. Rodrigues; Telmo G. D. Silva; Pedro B. P. S. Reis; Miguel Machuqueiro. "Extending the Stochastic Titration CpHMD to CHARMM36m". The Journal of Physical Chemistry B (2022): https://doi.org/10.1021/acs.jpcb.2c04529.
    10.1021/acs.jpcb.2c04529
  20. Pedro B.P.S. Reis; Marco Bertolini; Floriane Montanari; Walter Rocchia; Miguel Machuqueiro; Djork-Arné Clevert. "A Fast and Interpretable Deep Learning Approach for Accurate Electrostatics-Driven pKa Predictions in Proteins". Journal of Chemical Theory and Computation (2022): https://doi.org/10.1021/acs.jctc.2c00308.
    10.1021/acs.jctc.2c00308
  21. Pedro R. Magalhães; Pedro B. P. S. Reis; Diogo Vila-Viçosa; Miguel Machuqueiro; Bruno L. Victor. "Optimization of an in Silico Protocol Using Probe Permeabilities to Identify Membrane Pan-Assay Interference Compounds". Journal of Chemical Information and Modeling (2022): https://doi.org/10.1021/acs.jcim.2c00372.
    10.1021/acs.jcim.2c00372
  22. Nuno F. B. Oliveira; Miguel Machuqueiro. "Novel US-CpHMD Protocol to Study the Protonation-Dependent Mechanism of the ATP/ADP Carrier". Journal of Chemical Information and Modeling (2022): https://doi.org/10.1021/acs.jcim.2c00233.
    10.1021/acs.jcim.2c00233
  23. Viegas, Rui M. C.; Mestre, Ana S.; Mesquita, Elsa; Machuqueiro, Miguel; Andrade, Marta A.; Carvalho, Ana P.; Rosa, Maria João. Corresponding author: Mestre, Ana S.. "Key Factors for Activated Carbon Adsorption of Pharmaceutical Compounds from Wastewaters: A Multivariate Modelling Approach". Water 14 2 (2022): 166. http://dx.doi.org/10.3390/w14020166.
    Published • 10.3390/w14020166
  24. Reis, Pedro B P S; Clevert, Djork-Arné; Machuqueiro, Miguel. Corresponding author: Machuqueiro, Miguel. "pKPDB: a protein data bank extension database of pKa and pI theoretical values". Bioinformatics 38 1 (2022): 297-298. http://dx.doi.org/10.1093/bioinformatics/btab518.
    Published • 10.1093/bioinformatics/btab518
  25. Loureiro, Joana B.; Ribeiro, Rita; Nazareth, Nair; Ferreira, Tiago; Lopes, Elizabeth A.; Gama, Adelina; Machuqueiro, Miguel; et al. Corresponding author: Saraiva, Lucília. "Mutant p53 reactivator SLMP53-2 hinders ultraviolet B radiation-induced skin carcinogenesis". Pharmacological Research 175 (2022): 106026. http://dx.doi.org/10.1016/j.phrs.2021.106026.
    Published • 10.1016/j.phrs.2021.106026
  26. Bueschbell, Beatriz; Caniceiro, Ana Beatriz; Suzano, Pedro M.S.; Machuqueiro, Miguel; Rosário-Ferreira, Nícia; Moreira, Irina S.. Corresponding author: Moreira, Irina S.. "Network biology and artificial intelligence drive the understanding of the multidrug resistance phenotype in cancer". Drug Resistance Updates 60 (2022): 100811. http://dx.doi.org/10.1016/j.drup.2022.100811.
    Published • 10.1016/j.drup.2022.100811
  27. de Faria, Catarina Frazão; Moreira, Tânia; Lopes, Pedro; Costa, Henrique; Krewall, Jessica R.; Barton, Callie M.; Santos, Susana; et al. Corresponding author: Machuqueiro, Miguel. "Designing new antitubercular isoniazid derivatives with improved reactivity and membrane trafficking abilities". Biomedicine & Pharmacotherapy 144 (2021): 112362. http://dx.doi.org/10.1016/j.biopha.2021.112362.
    Published • 10.1016/j.biopha.2021.112362
  28. Rosário-Ferreira, Nícia; Baptista, Salete J.; Barreto, Carlos A. V.; Rodrigues, Filipe E. P.; Silva, Tomás F. D.; Ferreira, Sara G. F.; Vitorino, João N. M.; et al. Corresponding author: Machuqueiro, Miguel. "In Silico End-to-End Protein–Ligand Interaction Characterization Pipeline: The Case of SARS-CoV-2". ACS Synthetic Biology 10 11 (2021): 3209-3235. http://dx.doi.org/10.1021/acssynbio.1c00368.
    Published • 10.1021/acssynbio.1c00368
  29. Silva, Tomás F. D.; Vila-Viçosa, Diogo; Machuqueiro, Miguel. Corresponding author: Machuqueiro, Miguel. "Improved Protocol to Tackle the pH Effects on Membrane-Inserting Peptides". Journal of Chemical Theory and Computation 17 7 (2021): 3830-3840. http://dx.doi.org/10.1021/acs.jctc.1c00020.
    Published • 10.1021/acs.jctc.1c00020
  30. Rodrigues, Filipe E. P.; Figueira, António J.; Gomes, Cláudio M.; Machuqueiro, Miguel. Corresponding author: Machuqueiro, Miguel. "Computational Analysis of the Interactions between the S100B Extracellular Chaperone and Its Amyloid ß Peptide Client". International Journal of Molecular Sciences 22 7 (2021): 3629. http://dx.doi.org/10.3390/ijms22073629.
    Published • 10.3390/ijms22073629
  31. Cristóvão, Joana S.; Moreira, Guilherme G.; Rodrigues, Filipe E. P.; Carapeto, Ana P.; Rodrigues, Mário S.; Cardoso, Isabel; Ferreira, António E. N.; et al. Corresponding author: Gomes, Cláudio M.. "Cu2+-binding to S100B triggers polymerization of disulfide cross-linked tetramers with enhanced chaperone activity against amyloid-ß aggregation". Chemical Communications 57 3 (2021): 379-382. http://dx.doi.org/10.1039/d0cc06842j.
    Published • 10.1039/d0cc06842j
  32. Oliveira, Nuno F.B.; Rodrigues, Filipe E.P.; Vitorino, João N.M.; Loureiro, Rui J.S.; Faísca, Patrícia F.N.; Machuqueiro, Miguel. Corresponding author: Machuqueiro, Miguel. "Predicting stable binding modes from simulated dimers of the D76N mutant of ß2-microglobulin". Computational and Structural Biotechnology Journal 19 (2021): 5160-5169. http://dx.doi.org/10.1016/j.csbj.2021.09.003.
    Published • 10.1016/j.csbj.2021.09.003
  33. de Matos, Ana M.; Blázquez-Sánchez, M. Teresa; Bento-Oliveira, Andreia; de Almeida, Rodrigo F. M.; Nunes, Rafael; Lopes, Pedro E. M.; Machuqueiro, Miguel; et al. Corresponding author: Rauter, Amélia P.. "Glucosylpolyphenols as Inhibitors of Aß-Induced Fyn Kinase Activation and Tau Phosphorylation: Synthesis, Membrane Permeability, and Exploratory Target Assessment within the Scope of Type 2 Diabetes and Alzheimer’s Disease". Journal of Medicinal Chemistry 63 20 (2020): 11663-11690. http://dx.doi.org/10.1021/acs.jmedchem.0c00841.
    Published • 10.1021/acs.jmedchem.0c00841
  34. Reis, Pedro B. P. S.; Vila-Viçosa, Diogo; Rocchia, Walter; Machuqueiro, Miguel. Corresponding author: Machuqueiro, Miguel. "PypKa: A Flexible Python Module for Poisson–Boltzmann-Based pKa Calculations". Journal of Chemical Information and Modeling 60 10 (2020): 4442-4448. http://dx.doi.org/10.1021/acs.jcim.0c00718.
    Published • 10.1021/acs.jcim.0c00718
  35. Oliveira, Nuno F. B.; Pires, Inês D. S.; Machuqueiro, Miguel. Corresponding author: Machuqueiro, Miguel. "Improved GROMOS 54A7 Charge Sets for Phosphorylated Tyr, Ser, and Thr to Deal with pH-Dependent Binding Phenomena". Journal of Chemical Theory and Computation 16 10 (2020): 6368-6376. http://dx.doi.org/10.1021/acs.jctc.0c00529.
    Published • 10.1021/acs.jctc.0c00529
  36. Dallavalle, Sabrina; Dobricic, Vladimir; Lazzarato, Loretta; Gazzano, Elena; Machuqueiro, Miguel; Pajeva, Ilza; Tsakovska, Ivanka; Zidar, Nace; Fruttero, Roberta. Corresponding author: Fruttero, Roberta. "Improvement of conventional anti-cancer drugs as new tools against multidrug resistant tumors". Drug Resistance Updates 50 (2020): 100682. http://dx.doi.org/10.1016/j.drup.2020.100682.
    Published • 10.1016/j.drup.2020.100682
  37. Stark, Michal; Silva, Tomás F. D.; Levin, Guy; Machuqueiro, Miguel; Assaraf, Yehuda G.. Corresponding author: Assaraf, Yehuda G.. "The Lysosomotropic Activity of Hydrophobic Weak Base Drugs is Mediated via Their Intercalation into the Lysosomal Membrane". Cells 9 5 (2020): 1082. http://dx.doi.org/10.3390/cells9051082.
    Published • 10.3390/cells9051082
  38. João Franco Machado; Miguel Machuqueiro; Fernanda Marques; M. Paula Robalo; M. Fátima M. Piedade; M. Helena Garcia; João D. G. Correia; et al. Corresponding author: Morais, Tânia S.. "Novel “ruthenium cyclopentadienyl”–peptide conjugate complexes against human FGFR(+) breast cancer". Dalton Transactions 49 18 (2020): 5974-5987. https://doi.org/10.1039/D0DT00955E.
    Published • 10.1039/D0DT00955E
  39. Magalhães, P. R.; Machuqueiro, M.; Almeida, J. G.; Melo, J. G.; Cordeiro, M. N. D. S.; Cabo-Verde, S.; Gümüs, Z.H.; et al. Corresponding author: Melo, R.. "Dynamical Rearrangement of Human Epidermal Growth Factor Receptor 2 upon Antibody Binding: Effects on the Dimerization". Biomolecules 9 11 (2019): 706. http://dx.doi.org/10.3390/biom9110706.
    Published • 10.3390/biom9110706
  40. Laura Guedes; Pedro B. P. S. Reis; Miguel Machuqueiro; Asma Ressaissi; Rita Pacheco; Maria Luísa Serralheiro. Corresponding author: Maria Luísa Serralheiro. "Bioactivities of Centaurium erythraea (Gentianaceae) Decoctions: Antioxidant Activity, Enzyme Inhibition and Docking Studies". Molecules (2019): https://doi.org/10.3390/molecules24203795.
    Published • 10.3390/molecules24203795
  41. Assaraf, Yehuda G.; Brozovic, Anamaria; Gonçalves, Ana Cristina; Jurkovicova, Dana; Line, Aija; Machuqueiro, Miguel; Saponara, Simona; et al. Corresponding author: Vasconcelos, M. Helena. "The multi-factorial nature of clinical multidrug resistance in cancer". Drug Resistance Updates 46 (2019): 100645. http://dx.doi.org/10.1016/j.drup.2019.100645.
    Published • 10.1016/j.drup.2019.100645
  42. Rui J. S. Loureiro; Diogo Vila-Viçosa; Miguel Machuqueiro; Eugene I. Shakhnovich; Patrícia F. N. Faísca. Corresponding author: Patrícia F. N. Faísca. "The Early Phase of ß2m Aggregation: An Integrative Computational Study Framed on the D76N Mutant and the ¿N6 Variant". Biomolecules (2019): https://doi.org/10.3390/biom9080366.
    Published • 10.3390/biom9080366
  43. Diogo Vila-Viçosa; Pedro B. P. S. Reis; António M. Baptista; Chris Oostenbrink; Miguel Machuqueiro. Corresponding author: Diogo Vila-Viçosa. "A pH Replica Exchange Scheme in the Stochastic Titration Constant-pH MD Method". Journal of Chemical Theory and Computation (2019): https://doi.org/10.1021/acs.jctc.9b00030.
    Published • 10.1021/acs.jctc.9b00030
  44. Filipa Pires; Vananélia P. N. Geraldo; Bárbara Rodrigues; António de Granada-Flor; Rodrigo F. M. de Almeida; Osvaldo N. Oliveira, Jr.; Bruno L. Victor; Miguel Machuqueiro; Maria Raposo. Corresponding author: Maria Raposo. "Evaluation of EGCG Loading Capacity in DMPC Membranes". Langmuir (2019): https://doi.org/10.1021/acs.langmuir.9b00372.
    Published • 10.1021/acs.langmuir.9b00372
  45. Quintal, Susana; Pires da Silva, Maria João; Martins, Soraia R. M.; Sales, Rita; Félix, Vítor; Drew, Michael G. B.; Meireles, Margarida; et al. Corresponding author: Calhorda, Maria José. "Molybdenum(ii) complexes with p-substituted BIAN ligands: synthesis, characterization, biological activity and computational study". Dalton Transactions 48 23 (2019): 8449-8463. http://dx.doi.org/10.1039/c9dt00469f.
    Published • 10.1039/c9dt00469f
  46. Catarina Dias; João P. Pais; Rafael Nunes; Maria-Teresa Blázquez-Sánchez; Joaquim T. Marquês; Andreia F. Almeida; Patrícia Serra; et al. Corresponding author: Amélia P. Rauter. "Sugar-based bactericides targeting phosphatidylethanolamine-enriched membranes". Nature Communications 9 1 (2018): https://doi.org/10.1038/s41467-018-06488-4.
    Published • 10.1038/s41467-018-06488-4
  47. Tomás F. D. Silva; Diogo Vila-Viçosa; Pedro B. P. S. Reis; Bruno L. Victor; Matthias Diem; Chris Oostenbrink; Miguel Machuqueiro. Corresponding author: Miguel Machuqueiro. "The Impact of Using Single Atomistic Long-Range Cutoff Schemes with the GROMOS 54A7 Force Field". Journal of Chemical Theory and Computation (2018): https://doi.org/10.1021/acs.jctc.8b00758.
    Published • 10.1021/acs.jctc.8b00758
  48. Rafael Nunes; Diogo Vila-Viçosa; Miguel Machuqueiro; Paulo J. Costa. Corresponding author: Paulo J. Costa. "Biomolecular Simulations of Halogen Bonds with a GROMOS Force Field". Journal of Chemical Theory and Computation (2018): https://doi.org/10.1021/acs.jctc.8b00278.
    Published • 10.1021/acs.jctc.8b00278
  49. Helena Gaspar; Soraia Bronze; Catarina Oliveira; Bruno L. Victor; Miguel Machuqueiro; Rita Pacheco; Maria João Caldeira; Susana Santos. Corresponding author: Susana Santos. "Proactive response to tackle the threat of emerging drugs: Synthesis and toxicity evaluation of new cathinones". Forensic Science International 290 (2018): 146-156. https://doi.org/10.1016/j.forsciint.2018.07.001.
    Published • 10.1016/j.forsciint.2018.07.001
  50. Diogo Vila-Viçosa; Tomás F. D. Silva; Gregory Slaybaugh; Yana K. Reshetnyak; Oleg A. Andreev; Miguel Machuqueiro. Corresponding author: Miguel Machuqueiro. "Membrane-Induced pKa Shifts in wt-pHLIP and Its L16H Variant". Journal of Chemical Theory and Computation (2018): https://doi.org/10.1021/acs.jctc.8b00102.
    Published • 10.1021/acs.jctc.8b00102
  51. Pedro B. P. S. Reis; Diogo Vila-Viçosa; Sara R. R. Campos; António M. Baptista; Miguel Machuqueiro. Corresponding author: Miguel Machuqueiro. "Role of Counterions in Constant-pH Molecular Dynamics Simulations of PAMAM Dendrimers". ACS Omega (2018): https://doi.org/10.1021/acsomega.7b01708.
    Published • 10.1021/acsomega.7b01708
  52. Marques, S. C. R.; Mestre, A. S.; Machuqueiro, M.; Gotvajn, A. Z.; Marinsek, M.; Carvalho, A. P.; Marques, S.C.R.; et al. Corresponding author: Carvalho, A. P.. "Apple tree branches derived activated carbons for the removal of beta-blocker atenolol". Chemical Engineering Journal Accepted (2018): 669-678. https://doi.org/10.1016/j.cej.2018.01.076.
    Published • https://doi.org/10.1016/j.cej.2018.01.076
  53. Filipe, Hugo A L; Sousa, Carla; Marques, Joaquim T; Vila-Vicosa, Diogo; de Granada-Flor, Antonio; Viana, Ana S; Santos, M Soledade C S; Machuqueiro, Miguel; de Almeida, Rodrigo F M. Corresponding author: de Almeida, Rodrigo F M. "Differential targeting of membrane lipid domains by caffeic acid and its ester derivatives.". Free radical biology & medicine 115 (2018): 232-245. http://dx.doi.org/10.1016/j.freeradbiomed.2017.12.002.
    Published • 10.1016/j.freeradbiomed.2017.12.002
  54. Brito, Elsa; Gomes, Emma; Fale, Pedro L; Borges, Carlos; Pacheco, Rita; Teixeira, Vitor; Machuqueiro, Miguel; Ascensao, Lia; Serralheiro, Maria Luisa M. Corresponding author: Fale, Pedro L. "Bioactivities of decoctions from Plectranthus species related to their traditional use on the treatment of digestive problems and alcohol intoxication.". Journal of ethnopharmacology 220 (2018): 147-154. https://doi.org/10.1016/j.jep.2018.04.006.
    Published • 10.1016/j.jep.2018.04.006
  55. Jesus, Ana R.; Vila-Vicosa, Diogo; Machuqueiro, Miguel; Marques, Ana P.; Dore, Timothy M.; Rauter, Amelia P.. Corresponding author: Dore, Timothy M.. "Targeting Type 2 Diabetes with C-Glucosyl Dihydrochalcones as Selective Sodium Glucose Co-Transporter 2 (SGLT2) Inhibitors: Synthesis and Biological Evaluation". Journal of Medicinal Chemistry 60 2 (2017): 568-579. http://dx.doi.org/10.1021/acs.jmedchem.6b01134.
    Published • 10.1021/acs.jmedchem.6b01134
  56. Machuqueiro, Miguel; Victor, Bruno; Switala, Jacek; Villanueva, Jacylyn; Rovira, Carme; Fita, Ignacio; Loewen, Peter C.. Corresponding author: Loewen, Peter C.. "The Catalase Activity of Catalase-Peroxidases Is Modulated by Changes in the pK(a) of the Distal Histidine". Biochemistry 56 17 (2017): 2271-2281. http://dx.doi.org/10.1021/acs.biochem.6b01276.
    Published • 10.1021/acs.biochem.6b01276
  57. Vila-Vicosa, Diogo; Victor, Bruno L.; Ramos, Jorge; Machado, Diana; Viveiros, Miguel; Switala, Jacek; Loewen, Peter C.; et al. Corresponding author: Martins, Filomena. "Insights on the Mechanism of Action of INH-C-10 as an Antitubercular Prodrug". Molecular Pharmaceutics 14 12 (2017): 4597-4605. http://dx.doi.org/10.1021/acs.molpharmaceut.7b00719.
    Published • 10.1021/acs.molpharmaceut.7b00719
  58. Ressaissi, Asma; Attia, Nebil; Fale, Pedro Luis; Pacheco, Rita; Victor, Bruno L.; Machuqueiro, Miguel; Serralheiro, Maria Luisa M.. Corresponding author: Serralheiro, Maria Luisa M.. "Isorhamnetin derivatives and piscidic acid for hypercholesterolemia: cholesterol permeability, HMG-CoA reductase inhibition, and docking studies". Archives of Pharmacal Research 40 11 (2017): 1278-1286. https://doi.org/10.1007/s12272-017-0959-1.
    Published • 10.1007/s12272-017-0959-1
  59. Loureiro, Rui J. S.; Vila-Vicosa, Diogo; Machuqueiro, Miguel; Shakhnovich, Eugene I.; Faisca, Patricia F. N.. Corresponding author: Faisca, Patricia F. N.. "A tale of two tails: The importance of unstructured termini in the aggregation pathway of beta 2-microglobulin". Proteins-Structure Function and Bioinformatics 85 11 (2017): 2045-2057. http://dx.doi.org/10.1002/prot.25358.
    Published • 10.1002/prot.25358
  60. Silva, Leticia; Rodrigues, Ana Margarida; Ciriani, Marina; Vieira Fale, Pedro Luis; Teixeira, Vitor; Madeira, Paulo; Machuqueiro, Miguel; et al. Corresponding author: Marques Serralheiro, Maria Luisa. "Antiacetylcholinesterase activity and docking studies with chlorogenic acid, cynarin and arzanol from Helichrysum stoechas (Lamiaceae)". Medicinal Chemistry Research 26 11 (2017): 2942-2950. http://dx.doi.org/10.1007/s00044-017-1994-7.
    Published • 10.1007/s00044-017-1994-7
  61. Silva, Letícia; Rodrigues, Ana M.; Ciriani, Marina; Falé, Pedro Luís Vieira; Teixeira, Vitor; Madeira, Paulo; Machuqueiro, Miguel; et al. "Antiacetylcholinesterase activity and docking studies with chlorogenic acid, cynarin and arzanol from Helichrysum stoechas (Asteraceae)". (2017): http://hdl.handle.net/10400.21/7396.
    10.1007/s00044-018-2159-z
  62. Filipe, Luis C. S.; Campos, Sara R. R.; Machuqueiro, Miguel; Darbre, Tamis; Baptista, Antonio M.. Corresponding author: Baptista, Antonio M.. "Structuring Peptide Dendrimers through pH Modulation and Substrate Binding". Journal of Physical Chemistry B 120 38 (2016): 10138-10152. http://dx.doi.org/10.1021/acs.jpcb.6b05905.
    Published • 10.1021/acs.jpcb.6b05905
  63. Teixeira, Vitor H.; Capacho, Ana Sofia C.; Machuqueiro, Miguel. Corresponding author: Machuqueiro, Miguel. "The role of electrostatics in TrxR electron transfer mechanism: A computational approach". Proteins-Structure Function and Bioinformatics 84 12 (2016): 1836-1843. http://dx.doi.org/10.1002/prot.25166.
    Published • 10.1002/prot.25166
  64. Vilas-Boas, Filipe; Bagulho, Ana; Tenente, Rita; Teixeira, Vitor H.; Martins, Gabriel; da Costa, Goncalo; Jeronimo, Ana; et al. Corresponding author: Real, Carla. "Hydrogen peroxide regulates cell adhesion through the redox sensor RPSA". Free Radical Biology and Medicine 90 (2016): 145-157. http://dx.doi.org/10.1016/j.freeradbiomed.2015.11.019.
    Published • 10.1016/j.freeradbiomed.2015.11.019
  65. Teixeira, Vitor H.; Vila-Vicosa, Diogo; Reis, Pedro B. P. S.; Machuqueiro, Miguel. Corresponding author: Machuqueiro, Miguel. "pKa Values of Titrable Amino Acids at the Water/Membrane Interface". Journal of Chemical Theory and Computation 12 3 (2016): 930-934. http://dx.doi.org/10.1021/acs.jctc.5b01114.
    Published • 10.1021/acs.jctc.5b01114
  66. Ressaissi, A.; Attia, N.; Falé, P. L. V.; Pacheco, R.; Teixeira, V. H.; Machuqueiro, M.; Borges, C.; Serralheiro, M. L. M.. Corresponding author: Serralheiro, M. L. M.. "Aqueous extracts from nopal (Opuntia Ficus-Indica): antiacetylcholinesterase and antioxidant activity from phenolic bioactive compounds". Int J Green Herb Chem 5 (2016): 337-348. http://ijghc.com/download_frontend.php?id=205&table=Green%20Chemistry.
    Published
  67. Filipe, Luis C. S.; Machuqueiro, Miguel; Darbre, Tamis; Baptista, Antonio M.. Corresponding author: Baptista, Antonio M.. "Exploring the Structural Properties of Positively Charged Peptide Dendrimers". Journal of Physical Chemistry B 120 43 (2016): 11323-11330. http://dx.doi.org/10.1021/acs.jpcb.6b09156.
    Published • 10.1021/acs.jpcb.6b09156
  68. Magalhaes, Pedro R.; Machuqueiro, Miguel; Baptista, Antonio M.. Corresponding author: Baptista, Antonio M.. "Constant-pH Molecular Dynamics Study of Kyotorphin in an Explicit Bilayer". Biophysical Journal 108 9 (2015): 2282-2290. http://dx.doi.org/10.1016/j.bpj.2015.03.052.
    Published • 10.1016/j.bpj.2015.03.052
  69. Teixeira, Vitor H.; Ventura, Cristina; Leitao, Ruben; Rafols, Clara; Bosch, Elisabeth; Martins, Filomena; Machuqueiro, Miguel. Corresponding author: Machuqueiro, Miguel. "Molecular Details of INH-C-10 Binding to wt KatG and Its S315T Mutant". Molecular Pharmaceutics 12 3 (2015): 898-909. http://dx.doi.org/10.1021/mp500736n.
    Published • 10.1021/mp500736n
  70. Vila-Vicosa, Diogo; Teixeira, Vitor H.; Baptista, Antonio M.; Machuqueiro, Miguel. Corresponding author: Machuqueiro, Miguel. "Constant-pH MD Simulations of an Oleic Acid Bilayer". Journal of Chemical Theory and Computation 11 5 (2015): 2367-2376. http://dx.doi.org/10.1021/acs.jctc.5b00095.
    Published • 10.1021/acs.jctc.5b00095
  71. Santos, Hugo A. F.; Vila-Vicosa, Diogo; Teixeira, Vitor H.; Baptista, Antonio M.; Machuqueiro, Miguel. Corresponding author: Machuqueiro, Miguel. "Constant-pH MD Simulations of DMPA/DMPC Lipid Bilayers". Journal of Chemical Theory and Computation 11 12 (2015): 5973-5979. http://dx.doi.org/10.1021/acs.jctc.5b00956.
    Published • 10.1021/acs.jctc.5b00956
  72. Carvalheda, C.A.; Campos, S.R.R.; Machuqueiro, M.; Baptista, A.M.. "Correction to "structural effects of pH and deacylation on surfactant protein C in an organic solvent mixture: A constant-pH MD study"". Journal of Chemical Information and Modeling 55 1 (2015): 206-206. http://www.scopus.com/inward/record.url?eid=2-s2.0-84921826482&partnerID=MN8TOARS.
    10.1021/ci5007454
  73. Vila-Vicosa, Diogo; Francesconi, Oscar; Machuqueiro, Miguel. Corresponding author: Machuqueiro, Miguel. "Why a diaminopyrrolic tripodal receptor binds mannosides in acetonitrile but not in water?". Beilstein Journal of Organic Chemistry 10 (2014): 1513-1523. http://dx.doi.org/10.3762/bjoc.10.156.
    Published • 10.3762/bjoc.10.156
  74. Teixeira, Vitor H.; Vila-Vicosa, Diogo; Baptista, Antonio M.; Machuqueiro, Miguel. Corresponding author: Machuqueiro, Miguel. "Protonation of DMPC in a Bilayer Environment Using a Linear Response Approximation". Journal of Chemical Theory and Computation 10 5 (2014): 2176-2184. http://dx.doi.org/10.1021/ct5000082.
    Published • 10.1021/ct5000082
  75. Vila-Vicosa, Diogo; Teixeira, Vitor H.; Santos, Hugo A. F.; Baptista, Antonio M.; Machuqueiro, Miguel. Corresponding author: Machuqueiro, Miguel. "Treatment of Ionic Strength in Biomolecular Simulations of Charged Lipid Bilayers". Journal of Chemical Theory and Computation 10 12 (2014): 5483-5492. http://dx.doi.org/10.1021/ct500680q.
    Published • 10.1021/ct500680q
  76. Estacio, Silvia G.; Krobath, Heinrich; Vila-Vicosa, Diogo; Machuqueiro, Miguel; Shakhnovich, Eugene I.; Faisca, Patricia F. N.. Corresponding author: Faisca, Patricia F. N.. "A Simulated Intermediate State for Folding and Aggregation Provides Insights into Delta N6 beta(2)-Microglobulin Amyloidogenic Behavior". Plos Computational Biology 10 5 (2014): http://dx.doi.org/10.1371/journal.pcbi.1003606.
    Published • 10.1371/journal.pcbi.1003606
  77. Mestre, Ana S.; Machuqueiro, Miguel; Silva, Mariline; Freire, Ruben; Fonseca, Isabel M.; Santos, M. Soledade C. S.; Calhorda, Maria Jose; Carvalho, Ana P.. Corresponding author: Carvalho, Ana P.. "Influence of activated carbons porous structure on iopamidol adsorption". Carbon 77 (2014): 607-615. http://dx.doi.org/10.1016/j.carbon.2014.05.065.
    Published • 10.1016/j.carbon.2014.05.065
  78. Martins, Alice; Santos, Maria S.; Dias, Catarina; Serra, Patricia; Cachatra, Vasco; Pais, Joao; Caio, Joao; et al. Corresponding author: Rauter, Amelia P.. "Tuning the Bioactivity of Tensioactive Deoxy Glycosides to Structure: Antibacterial Activity Versus Selective Cholinesterase Inhibition Rationalized by Molecular Docking". European Journal of Organic Chemistry 8 (2013): 1448-1459. http://dx.doi.org/10.1002/ejoc.201201520.
    10.1002/ejoc.201201520
  79. Filipe, Luis C. S.; Machuqueiro, Miguel; Darbre, Tamis; Baptista, Antonio M.. Corresponding author: Baptista, Antonio M.. "Unraveling the Conformational Determinants of Peptide Dendrimers Using Molecular Dynamics Simulations". Macromolecules 46 23 (2013): 9427-9436. http://dx.doi.org/10.1021/ma401574b.
    Published • 10.1021/ma401574b
  80. Vila-Vicosa, Diogo; Teixeira, Vitor H.; Santos, Hugo A. F.; Machuqueiro, Miguel. Corresponding author: Machuqueiro, Miguel. "Conformational Study of GSH and GSSG Using Constant-pH Molecular Dynamics Simulations". Journal of Physical Chemistry B 117 25 (2013): 7507-7517. http://dx.doi.org/10.1021/jp401066v.
    Published • 10.1021/jp401066v
  81. Carvalheda, Catarina A.; Campos, Sara R. R.; Machuqueiro, Miguel; Baptista, Antonio M.. Corresponding author: Baptista, Antonio M.. "Structural Effects of pH and Deacylation on Surfactant Protein C in an Organic Solvent Mixture: A Constant-pH MD Study". Journal of Chemical Information and Modeling 53 11 (2013): 2979-2989. http://dx.doi.org/10.1021/ci400479c.
    Published • 10.1021/ci400479c
  82. Henriques, Joao; Costa, Paulo J.; Calhorda, Maria Jose; Machuqueiro, Miguel. Corresponding author: Machuqueiro, Miguel. "Charge Parametrization of the DvH-c(3) Heme Group: Validation Using Constant-(pH,E) Molecular Dynamics Simulations". Journal of Physical Chemistry B 117 1 (2013): 70-82. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000313220600008&KeyUID=WOS:000313220600008.
    Published • 10.1021/jp3082134
  83. Vila-Vicosa, Diogo; Campos, Sara R. R.; Baptista, Antonio M.; Machuqueiro, Miguel. Corresponding author: Machuqueiro, Miguel. "Reversibility of Prion Misfolding: Insights from Constant-pH Molecular Dynamics Simulations". Journal of Physical Chemistry B 116 30 (2012): 8812-8821. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000306989800009&KeyUID=WOS:000306989800009.
    Published • 10.1021/jp3034837
  84. Gamelas, Carla A.; Bandeira, Nuno A. G.; Pereira, Claudia C. L.; Calhorda, Maria Jose; Herdtweck, Eberhardt; Machuqueiro, Miguel; Romao, Carlos C.; Veiros, Luis F.. Corresponding author: Calhorda, Maria Jose. "Indenyl ring slippage in crown thioether complexes [IndMo(CO)2L]+ and C-S activation of trithiacyclononane: Experimental and theoretical studies". Dalton Transactions 40 40 (2011): 10513-10525. http://dx.doi.org/10.1039/C1DT10607D.
    10.1039/c1dt10607d
  85. Machuqueiro, Miguel; Baptista, Antonio M.. Corresponding author: Baptista, Antonio M.. "Is the prediction of pK(a) values by constant-pH molecular dynamics being hindered by inherited problems?". Proteins-Structure Function and Bioinformatics 79 12 (2011): 3437-3447. http://dx.doi.org/10.1002/prot.23115.
    Published • 10.1002/prot.23115
  86. Filipe, LCS; Machuqueiro, M; Baptista, AM. Corresponding author: Baptista, AM. "Unfolding the Conformational Behavior of Peptide Dendrimers: Insights from Molecular Dynamics Simulations". Journal of the American Chemical Society 133 13 (2011): 5042-5052. http://dx.doi.org/10.1021/ja111001v.
    10.1021/ja111001v
  87. Campos, SRR; Machuqueiro, M; Baptista, AM. Corresponding author: Baptista, AM. "Constant-pH Molecular Dynamics Simulations Reveal a beta-Rich Form of the Human Prion Protein". Journal of Physical Chemistry B 114 39 (2010): 12692-12700. http://dx.doi.org/10.1021/jp104753t.
    10.1021/jp104753t
  88. Machuqueiro, M; Campos, SRR; Soares, CM; Baptista, AM. Corresponding author: Baptista, AM. "Membrane-Induced Conformational Changes of Kyotorphin Revealed by Molecular Dynamics Simulations". Journal of Physical Chemistry B 114 35 (2010): 11659-11667. http://dx.doi.org/10.1021/jp104418g.
    Published • 10.1021/jp104418g
  89. Machuqueiro, M; Baptista, AM. Corresponding author: Baptista, AM. "Molecular Dynamics at Constant pH and Reduction Potential: Application to Cytochrome c(3)". Journal of the American Chemical Society 131 35 (2009): 12586-12594. http://dx.doi.org/10.1021/ja808463e.
    Published • 10.1021/ja808463e
  90. Machuqueiro, M; Baptista, AM. Corresponding author: Baptista, AM. "Acidic range titration of HEWL using a constant-pH molecular dynamics method". Proteins-Structure Function and Bioinformatics 72 1 (2008): 289-298. http://dx.doi.org/10.1002/prot.21923.
    Published • 10.1002/prot.21923
  91. Machuqueiro, M; Baptista, AM. Corresponding author: Baptista, AM. "The pH-dependent conformational states of kyotorphin: A constant-pH molecular dynamics study". Biophysical Journal 92 6 (2007): 1836-1845. http://dx.doi.org/10.1529/biophysj.106.092445.
    Published • 10.1529/biophysj.106.092445
  92. Machuqueiro, M; Baptista, AM. Corresponding author: Baptista, AM. "Constant-pH molecular dynamics with ionic strength effects: Protonation-conformation coupling in decalysine". Journal of Physical Chemistry B 110 6 (2006): 2927-2933. http://dx.doi.org/10.1021/jp056456q.
    Published • 10.1021/jp056456q
  93. Fernandez-Lopez, R; Kofoed, J; Machuqueiro, M; Darbre, T. Corresponding author: Darbre, T. "A selective direct aldol reaction in aqueous media catalyzed by zinc-proline". European Journal of Organic Chemistry 24 (2005): 5268-5276. http://dx.doi.org/10.1002/ejoc.200500352.
    Published • 10.1002/ejoc.200500352
  94. Teixeira, VH; Cunha, CA; Machuqueiro, M; Oliveira, ASF; Victor, BL; Soares, CM; Baptista, AM. Corresponding author: Baptista, AM. "On the use of different dielectric constants for computing individual and pairwise terms in Poisson-Boltzmann studies of protein ionization equilibrium". Journal of Physical Chemistry B 109 30 (2005): 14691-14706. http://dx.doi.org/10.1021/jp052259f.
    Published • 10.1021/jp052259f
  95. Kofoed, Jacob; Machuqueiro, Miguel; Reymond, Jean-Louis; Darbre, Tamis. Corresponding author: Darbre, Tamis. "Zinc–proline catalyzed pathway for the formation of sugars". Chem. Commun. 13 (2004): 1540-1541. http://dx.doi.org/10.1039/b404465g.
    10.1039/b404465g
  96. Darbre, Tamis; Machuqueiro, Miguel. Corresponding author: Darbre, Tamis. "Zn-Proline catalyzed direct aldol reaction in aqueous media". Chemical Communications 9 (2003): 1090-1091. http://dx.doi.org/10.1039/b301117h.
    Published • 10.1039/b301117h
  97. Machuqueiro, Miguel; Darbre, Tamis. Corresponding author: Darbre, Tamis. "Zinc mediated methyl transfer from trimethyl phosphate to chelating and non-chelating alkyl thiols. Model for Zn-dependent methyltransferases". Journal of Inorganic Biochemistry 94 1-2 (2003): 193-196. http://dx.doi.org/10.1016/s0162-0134(02)00625-6.
    10.1016/s0162-0134(02)00625-6

Other

Other output
  1. PypKa Server: online pKa predictions and biomolecular structure preparation with precomputed data from PDB and AlphaFold DB. 2024. Pedro Reis; Djork-Arné Clevert; Miguel Machuqueiro. https://doi.org/10.1093/nar/gkae255.
    10.1093/nar/gkae255
  2. Understanding P-gp inhibition by RuCp compounds using a Molecular Docking protocol. Oral presentation given at the 2nd 3D-BIOINFO-PT annual meeting.. 2023. Sequeira, João G. N.; Ricardo G. Teixeira; Oliveira, N. F. B.; Valente, Andreia; Machuqueiro, Miguel.
  3. Extending Stochastic Titration CpHMD to AMBER14SB Force Field for Enhanced Drug Discovery. Oral communication given at Protein Electrostatics 2023, in Genova IT.. 2023. Sequeira, João G. N.; Roitberg, Adrian; Machuqueiro, Miguel.
  4. Extending the stochastic titration CpHMD to the AMBER14SB force field for future search of non-opioid analgesics. Oral communication at the FAME2023 conference in Tampa Florida.. 2023. Sequeira, João G. N.; Roitberg, Adrian; Machuqueiro, Miguel.
  5. A new ruthenium-cyclopentadienyl compound as a promising cancer MDR reversing agent. Oral communication given at CQE Days 2023.. 2023. Valente, Andreia; Ricardo G. Teixeira; Maximiano, Inês; Oliveira, N. F. B.; Sequeira, João G. N.; Antunes A; Machuqueiro, Miguel.
  6. Extending the stochastic titration CpHMD to the CHARMM36m and AMBER14SB force fields. Oral Communication given at the 3D-BioInfo-PT annual meeting.. 2022. Sequeira, João G. N.; Filipe E. P. Rodrigues; Telmo G. D. Silva; Reis, Pedro B P S; Machuqueiro, Miguel.
  7. High-throughput virtual screening to identify non-covalent inhibitors of CRM1 with potential antitumor. Oral Communication given at the 6ª Conferência Anual da RedeSAÚDE.. 2022. Sequeira, João G. N.; Machuqueiro, Miguel.
  8. CpHMD battle: GROMOS54A7 vs CHARMM36m. Oral communication at the Protein Electrostatics 2022 remote meeting.. 2022. Sequeira, João G. N.; Filipe E. P. Rodrigues; Reis, Pedro B P S; Machuqueiro, Miguel.
Activities

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2021 - 2023 Computational biophysics evaluation of promising smart metallodrug delivery systems
Supervisor of Inês Domingos da Silva Pires
 Biochemistry (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2018 - 2023 In silico tumor-targeting technologies for the evasion of acidity-induced multidrug resistance
Supervisor of Tomás Fernandes da Silva
 Theoretical Biochemistry (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2018 - 2023 A new generation of user-friendly and machine learning-accelerated methods for protein pKa calculations
Supervisor of Pedro de Brito Pires Santos Reis
 Theoretical Biochemistry (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2022 PyBindE: Development of a Simple Python MM-PBSA Implementation for Estimating Protein-Protein and Protein-Ligand Binding Energies
Supervisor of João Nuno Marques Vitorino
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2022 Developing a computational method to calculate pH-dependent membrane permeabilities for anti-tumour drugs
Supervisor of Pedro Miguel Sousa Suzano
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2022 High-throughput virtual screening to identify non-covalent inhibitors of CRM1 with anti-tumoral potential
Supervisor of João Gonçalo Nunes Sequeira
 Bioinformatics (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 - 2020 Study of the interaction between the amyloid B peptide and the S100B protein using computational techniques
Supervisor of Filipe Eduardo Pequito Rodrigues
 Biochemistry (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 - 2020 The role of electrostatics in the mechanism of ATP/ADP Carrier function: an in silico study
Supervisor of Nuno Filipe Baltazar Maia Costa de Oliveira
Universidade de Lisboa Faculdade de Ciências, Portugal
2016 - 2017 Computational study of pH-dependent membrane insertion mechanism of pHLIP peptides
Supervisor of Tomás Fernandes da Silva
Universidade de Lisboa Faculdade de Ciências, Portugal
2016 - 2017 Improving pKa calculations of membrane inserting amino acids using replica exchange CpHMD simulations
Supervisor of Pedro de Brito Pires Santos Reis
Universidade de Lisboa Faculdade de Ciências, Portugal
2016 - 2017 Encapsulamento da Catequina EGCG no Lipossoma: Múltiplas Abordagens
Co-supervisor of Bárbara Rodrigues
Universidade Nova de Lisboa Departamento de Física, Portugal
2011 - 2016 Studying the structural features of peptide dendrimers using a combined computational and experimental approach
Co-supervisor of Luís Carlos Santos Filipe
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2014 - 2015 Synthesis of new antibiotic glycosides and computational studies on their interaction with model lipid bilayers
Supervisor of Rafael de Santana Nunes
Universidade de Lisboa Faculdade de Ciências, Portugal
2011 - 2015 Molecular modeling and simulation of pH effects in lipid bilayers
Supervisor of Diogo Ruivo dos Santos Vila Viçosa
 Theoretical Biochemistry (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2013 - 2014 Cyclodextrins as anti-asthmatic drug carriers: an in silico study
Supervisor of Bruno Emanuel de Sá Calçada
Universidade de Lisboa Faculdade de Ciências, Portugal
2012 - 2013 Constant-pH MD simulations of higher complexity lipid bilayer models: PA/PC binary mixtures
Supervisor of Hugo Alexandre Feiteira dos Santos
Universidade de Lisboa Faculdade de Ciências, Portugal
2011 - 2012 Avaliação in silico da tioredoxina redutase como alvo para terapia anti-tumoral
Supervisor of Ana Sofia Capacho
Universidade de Lisboa Faculdade de Ciências, Portugal
2010 - 2011 Study of pH-dependent misfolding of surfactant protein C using state-of-the-art molecular modelling techniques
Co-supervisor of Catarina Carvalheda Santos
Universidade de Lisboa Faculdade de Ciências, Portugal
2009 - 2010 Application of QM and MM methodologies to cytochrome c3: charge parametrization of the heme group for classic force fields
Supervisor of João Manuel Almeida Henriques
Universidade de Lisboa Faculdade de Ciências, Portugal
2009 - 2010 Reversibility of prion misfolding by constant-pH molecular dynamics simulations
Supervisor of Diogo Vila Viçosa
Universidade de Lisboa Faculdade de Ciências, Portugal

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2023/01/04 Overcoming Multidrug Resistance: search for human P-glycoprotein modulators and insights on drug efflux mechanism
(Thesis) Main arguer
 Cátia Alexandra Marques Bonito Ferreira (PhD)
Universidade do Porto Faculdade de Ciências, Portugal
2022/12/12 Analysis of residue interaction networks in molecular dynamics simulations
(Thesis) Main arguer
 Gonçalo Miguel Fonseca Monteiro (Master)
Instituto Politécnico de Setúbal Escola Superior de Tecnologia do Barreiro, Portugal
2021/11/30 SARS-CoV-2 membrane protein: from genomic data to structural new insights
(Thesis) Main arguer
 Manuel Maria Moura Neves Moreira Pires (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2021/06/22 Computational studies addressed to multifunctional enzyme complexes
(Thesis) Main arguer
 Carla Sílvia Silva Teixeira (PhD)
Universidade do Porto Faculdade de Ciências, Portugal
2020/12/10 The structural and functional role of CACNG2 mutations in psychiatric disorders
(Thesis) Main arguer
 Raquel Pina Gouveia (Master)
Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal
2019 Disclosing the aggregation mechanism of ß2-microglobulin in amyloid disease
(Thesis) Arguer
 Rui Loureiro (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2018 Molecular modeling study of beta-lactogrlobulin dimerization: a first step to hypoallergen design for immunotherapy
(Thesis) Main arguer
 Lucie da Rocha (Master)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2017 Reversing multidrug resistance (MDR) in cancer cells by targeting P-glycoprotein (Pgp)— Insights into the mechanism of MDR reversal from in silico Pgp modeling
(Thesis) Arguer
 Ricardo José Ferreira (PhD)
Universidade de Lisboa Faculdade de Farmácia, Portugal
2016 Modelação molecular/Bioinformática estrutural da hemaglutinina do virus influenza
(Thesis) Main arguer
 Jorge Antunes (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2013 Estudos de Inibição Enzimática
(Thesis) Main arguer
 Marta Perez Gomes (PhD)
Universidade do Porto, Portugal
2013 Theoretical investigation of the energy of olefin- and sila-olefin insertion/ß-H elimination reactions of two late transition metals – DFT MO calculations
(Thesis) Arguer
 Rita Ferro (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2012 Propriedades Electrónicas de Espécies Hidrofóbicas Micro-solvatadas e em Solução
(Thesis) Arguer
 Margarida Mateus (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2011 Molecular Modelling of transmembranar transporters for Chloride
(Thesis) Main arguer
 Igor Marques (Master)
Universidade de Aveiro, Portugal

Committee member

Activity description
Role 		Institution / Organization
2020/01/01 - 2024/12/31 Member of the Coordination team of the BioISI research unit. Responsible for the Computational Biology Thematic Line.
Other
 Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
2018/01/01 - 2019/12/31 Member of the Coordination team of the Centro de Química e Bioquímica research unit. Responsible for budget and funding management.
Other
 Universidade de Lisboa Centro de Química e Bioquímica, Portugal

Interview (tv / radio show)

Program Topic
2020/10/05 - Current 90 Segundos de Ciência Science

Journal scientific committee

Journal title (ISSN) Publisher
2018 - Current Journal of Computational Biophysics and Chemistry (2737-4165) World Scientific
2018 - Current The Journal of Membrane Biology (0022-2631) Springer
2013 - Current PLOS ONE (1932-6203) PLOS
Distinctions

Award

2023 CIÊNCIAS Research Day Award in the field of Chemical Sciences and Technologies
Universidade de Lisboa Faculdade de Ciências, Portugal

Other distinction

2016 Conference grant award (400 Euros) for the participation in the Protein Electrostatics Berlin in Berlin, Germany
Technische Universität Berlin Institut für Lebensmitteltechnologie und Lebensmittelchemie, Germany
2015 36 months grant for postdoctoral studies awarded by the Portuguese Foundation for Science and Technology in a highly competitive call.
Fundação para a Ciência e a Tecnologia, Portugal
2013 Conference grant award (900 Euros) for the participation in the 246th ACS Meeting in Indianapolis, USA
Fundação Luso-Americana, Portugal
2010 Conference grant award (1200 Euros) for the participation in the Proton Transfer Electrostatics in Telluride, CO, USA.
Fundação Luso-Americana, Portugal
2009 5 years contract under the Ciência2008 program by the Portuguese Foundation for Science and Technology in a highly competitive call.
Fundação para a Ciência e a Tecnologia, Portugal
2006 36 months grant for postdoctoral studies awarded by the Portuguese Foundation for Science and Technology in a highly competitive call.
Fundação para a Ciência e a Tecnologia, Portugal
2003 36 months grant for postdoctoral studies awarded by the Portuguese Foundation for Science and Technology in a highly competitive call.
Fundação para a Ciência e a Tecnologia, Portugal
1999 48 months grant for doctoral studies awarded by the Swiss National Science Foundation.
Schweizerischer Nationalfonds zur Förderung der wissenschaftlichen Forschung, Switzerland
1997 Prize awarded by the Portuguese office for the Ministry of Education under the program PRODEP for excellence in completion of undergraduate studies.
Universidade de Lisboa Faculdade de Ciências, Portugal