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Manuel is the head of the Multiscale Modeling lab within the MOSTMICRO unit of ITQB NOVA. His work is centered on elucidating the molecular-level details of lipid-lipid, lipid-protein, and protein-protein interactions; recent collaborations also focus on modeling bacterial structures. Manuel's research employs coarse-grained, atomistic, and hybrid molecular dynamic simulations, and tackles both the construction of models (as a developer within the Martini coarse-grain framework) and their application to biological questions. Manuel actively develops simulation and analysis software (he was a core developer of the MDAnalysis Python package), with emphasis on large-scale parallelization of analysis, and he is also Community Facilitator of 3D-BioInfo-PT (community of Portuguese structural computational biology researchers) within the BioData.pt infrastructure. Manuel's work, both in method development and in applied multidisciplinary research -- often in collaboration with experimental biochemistry and biology -- has ensured an impactful output, currently at an h-index of 32. As a Marie Curie Fellow, and later as a Dutch NWO VENI Fellow, Manuel carried out postdoctoral work at the Marrink lab, at the University of Groningen -- where he became involved in the development and application of Martini. Manuel pursued his Ph.D. on the molecular level interactions of antimicrobial peptides with cellular membranes, using spectroscopic techniques coupled to mathematical modeling, connecting biophysics to microbiology.
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Identification

Personal identification

Full name
Manuel Nuno de Sousa Pereira Simões de Melo

Citation names

  • Manuel N. Melo

Author identifiers

Ciência ID
2415-3C0E-8ED6
ORCID iD
0000-0001-6567-0513
Google Scholar ID
1aCENrwAAAAJ

Websites

Knowledge fields

  • Natural sciences - Biological Sciences - Biophysics
Education
Degree Classification
2006/01/01 - 2010/09/28
Concluded
 Bioquímica (Doutoramento)
Major in Biofísica Molecular
Universidade de Lisboa Faculdade de Ciências, Portugal
"Estudo do Mecanismo de Acção de Péptidos Microbicidas Ribossomais de Interesse Clínico" (THESIS/DISSERTATION)
 Aprovado com distinção e louvor
Affiliation

Science

Category
Host institution 		Employer
2019/06/16 - Current Auxiliary Researcher (Research) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2016/11/01 - 2019/06/15 Auxiliary Researcher (Research) Universidade Nova de Lisboa Microbiologia Molecular Estrutural e Celular, Portugal
Outputs

Publications

Book chapter
  1. Melo, Manuel N.. Corresponding author: Melo, Manuel N.. "Coarse-Grain Simulations of Membrane-Adsorbed Helical Peptides". In Computational Peptide Science, edited by Simonson, Thomas, 137-150. New York, United States: Springer US, 2022.
    Published • 10.1007/978-1-0716-1855-4_7
  2. Goga, N.; Rzepiela, A.; Melo, M.N.; de Vries, A.H.; Hadar, A.; Markvoort, A.J.; Nedea, S.; Berendsen, H.J.C.. "Methods for Multiscale Modeling of Membranes". In Advances in Planar Lipid Bilayers and Liposomes, 139-170. Elsevier, 2012.
    10.1016/b978-0-12-396533-2.00003-3
  3. Freire, João Miguel; Domingues, Marco M.; Matos, Joana; Melo, Manuel N.; Veiga, Ana Salomé; Santos, Nuno C.; Castanho, Miguel A. R. B.. "Quantifying molecular partition of charged molecules by Zeta-potential measurements". European Peptide Society, 2010.
Conference paper
  1. MELO, MANUEL. "MDAnalysis: a Python package for the rapid analysis of molecular dynamics simulations". 2016.
    10.25080/Majora-629e541a-00e
Conference poster
  1. Teixeira, Rita I.; Valério, Mariana; Borges-Araújo, Luis; Manuel N. Melo; Vicente, João B.; Lousa, Diana; Soares, Claudio M.. "Probing the RBD-ACE2 interactions to unlock the design of biologics against SARS-CoV-2 variants". Paper presented in PEGS Europe: Protein & Antibody Engineering Summit, 2023.
  2. Barriga, Rodrigo; Lotfi, Maryam; Pereira, Manuela M.; Manuel N. Melo. Corresponding author: Manuel N. Melo. "P-06.3-001 The analysis of Staphylococcus aureus' NDH-2 Coarse-Grain simulations might be the beginning to unveil a future therapeutical target". Paper presented in The Biochemistry Global Summit 25th IUBMB Congress 46th FEBS Congress 15th PABMB Congress, 2022.
    10.1002/2211-5463.13440
  3. Barriga, Rodrigo; Lotfi, Maryam; Pereira, Manuela M.; Manuel N. Melo. Corresponding author: Manuel N. Melo. "P49 The analysis of Staphylococcus aureus¿ NDH2 CoarseGrain simulations might be the beginning to unveil a future therapeutical target". Paper presented in 2nd Chem And Biochem Students Meeting, 2022.
  4. Teixeira, Rita I.; Valério, Mariana; Borges-Araújo, Luis; Manuel N. Melo; Vicente, João B.; Lousa, Diana; Soares, Claudio M.. Corresponding author: Lousa, Diana. "The impact of SARS-CoV-2 Omicron variant on the human ACE2 binding: a computational study". Paper presented in 2nd Portuguese Young Biophysicists¿ Meeting, Biophysics Festival 2022,, 2022.
  5. Mariana Valério; Diogo A. Mendonça; João M. Morais; Buga, Carolina C.; Carlos H. Cruz; Miguel A.R.B. Castanho; Manuel N. Melo; et al. "Together we fuse: Parainfluenza virus fusion peptides oligomerize to promote membrane fusion". Paper presented in Biophysics Festival 2022 - 2nd Meeting of Young Biophysicists, 2022.
  6. Barriga, Rodrigo; Lotfi, Maryam; Pereira, Manuela M.; Manuel N. Melo. Corresponding author: Manuel N. Melo. "P35 THE ANALYSIS OF STAPHYLOCOCCUS AUREUS¿ NDH2 COARSEGRAIN SIMULATIONS MIGHT BE THE BEGINNING TO UNVEIL A FUTURE THERAPEUTICAL TARGET". Paper presented in 2nd Meeting of Portuguese Young Biophysicists, 2022.
    10.5281/zenodo.6772805
  7. Barriga, Rodrigo; Lotfi, Maryam; Pereira, Manuela M.; Manuel N. Melo. Corresponding author: Manuel N. Melo. "P2 Parameterization of nucleotide cofactors and metabolites for the Martini 3 Coarse-Grain force field". Paper presented in VIII EJIBCE (Encontro de Jovens Investigadores de Biologia Computacional Estrutural), 2021.
  8. MELO, MANUEL. "Extending the Adress Multiscale Scheme for Protein and Bilayer Applications". 2016.
    10.1016/j.bpj.2015.11.3444
  9. MELO, MANUEL. "Computational Lipidomics and the Lipid Organization of Cell Envelopes". 2015.
    10.1016/j.bpj.2014.11.1875
Journal article
  1. Ana C. C. Barbosa; Sofia S. Venceslau; Delfim Ferreira; Sinje Neukirchen; Filipa L. Sousa; Manuel N. Melo; Inês A. C. Pereira. "Characterization of DsrD and its interaction with the DsrAB dissimilatory sulfite reductase". Protein Science (2024): https://doi.org/10.1002/pro.5222.
    10.1002/pro.5222
  2. Shashank Dadsena; Rodrigo Cuevas Arenas; Gonçalo Vieira; Susanne Brodesser; Manuel N. Melo; Ana J. García-Sáez. "Lipid unsaturation promotes BAX and BAK pore activity during apoptosis". Nature Communications (2024): https://doi.org/10.1038/s41467-024-49067-6.
    10.1038/s41467-024-49067-6
  3. Catarina J. Gaspar; Tiago Gomes; Joana C. Martins; Manuel N. Melo; Colin Adrain; Tiago N. Cordeiro; Pedro M. Domingos. "Xport-A functions as a chaperone by stabilizing the first five transmembrane domains of rhodopsin-1". iScience (2023): https://doi.org/10.1016/j.isci.2023.108309.
    10.1016/j.isci.2023.108309
  4. Marini, Eleonora; Olivença, Carmen; Ramalhete, Sara; Aguirre, Andrea Martinez; Ingle, Patrick; Melo, Manuel N.; Antunes, Wilson; et al. "A sporulation signature protease is required for assembly of the spore surface layers, germination and host colonization in Clostridioides difficile". PLOS Pathogens 19 11 (2023): e1011741. http://dx.doi.org/10.1371/journal.ppat.1011741.
    10.1371/journal.ppat.1011741
  5. Borges-Araújo, Luís; Borges-Araújo, Ana C.; Ozturk, Tugba Nur; Ramirez-Echemendia, Daniel P.; Fábián, Balázs; Carpenter, Timothy S.; Thallmair, Sebastian; et al. "Martini 3 Coarse-Grained Force Field for Cholesterol". Journal of Chemical Theory and Computation 19 20 (2023): 7387-7404. http://dx.doi.org/10.1021/acs.jctc.3c00547.
    Published • 10.1021/acs.jctc.3c00547
  6. Valdivieso González, David; Makowski, Marcin; Lillo, M. Pilar; Cao-García, Francisco J.; Melo, Manuel N.; Almendro-Vedia, Víctor G.; López-Montero, Iván. "Rotation of the c-Ring Promotes the Curvature Sorting of Monomeric ATP Synthases". Advanced Science 10 31 (2023): http://dx.doi.org/10.1002/advs.202301606.
    Published • 10.1002/advs.202301606
  7. J. Karl Spinti; Fernando Neiva Nunes; Manuel N. Melo. "Room for improvement in the initial martini 3 parameterization of peptide interactions". Chemical Physics Letters (2023): https://doi.org/10.1016/j.cplett.2023.140436.
    10.1016/j.cplett.2023.140436
  8. Erik Strandberg; Parvesh Wadhwani; Jochen Bürck; Patrick Anders; Christian Mink; Jonas van den Berg; Raffaele A. M. Ciriello; et al. "Temperature-Dependent Re-alignment of the Short Multifunctional Peptide BP100 in Membranes Revealed by Solid-State NMR Spectroscopy and Molecular Dynamics Simulations". ChemBioChem (2023): https://doi.org/10.1002/cbic.202200602.
    10.1002/cbic.202200602
  9. Siewert J. Marrink; Luca Monticelli; Manuel N. Melo; Riccardo Alessandri; D. Peter Tieleman; Paulo C. T. Souza. "Two decades of Martini: Better beads, broader scope". WIREs Computational Molecular Science (2023): https://doi.org/10.1002/wcms.1620.
    10.1002/wcms.1620
  10. Mariana Valério; Diogo A. Mendonça; João Morais; Carolina C. Buga; Carlos H. Cruz; Miguel A.R.B. Castanho; Manuel N. Melo; et al. "Parainfluenza Fusion Peptide Promotes Membrane Fusion by Assembling into Oligomeric Porelike Structures". ACS Chemical Biology (2022): https://doi.org/10.1021/acschembio.2c00208.
    10.1021/acschembio.2c00208
  11. Borges-Araújo, Luís; Souza, Paulo C. T.; Fernandes, Fábio; Melo, Manuel N.. "Improved Parameterization of Phosphatidylinositide Lipid Headgroups for the Martini 3 Coarse-Grain Force Field". Journal of Chemical Theory and Computation 18 1 (2021): 357-373. http://dx.doi.org/10.1021/acs.jctc.1c00615.
    Published • 10.1021/acs.jctc.1c00615
  12. Borges-Araújo, Luís; Domingues, Marco M.; Fedorov, Alexander; Santos, Nuno C.; Melo, Manuel N.; Fernandes, Fábio. "Acyl-chain saturation regulates the order of phosphatidylinositol 4,5-bisphosphate nanodomains". Communications Chemistry 4 1 (2021): http://dx.doi.org/10.1038/s42004-021-00603-1.
    Published • 10.1038/s42004-021-00603-1
  13. Mink, Christian; Strandberg, Erik; Wadhwani, Parvesh; Melo, Manuel N.; Reichert, Johannes; Wacker, Irene; Castanho, Miguel A. R. B.; Ulrich, Anne S.. "Overlapping Properties of the Short Membrane-Active Peptide BP100 With (i) Polycationic TAT and (ii) a-helical Magainin Family Peptides". Frontiers in Cellular and Infection Microbiology 11 (2021): http://dx.doi.org/10.3389/fcimb.2021.609542.
    Open access • 10.3389/fcimb.2021.609542
  14. Sousa, Filipe M.; Lima, Luís M. P.; Arnarez, Clément; Pereira, Manuela M.; Melo, Manuel N.. "Coarse-Grained Parameterization of Nucleotide Cofactors and Metabolites: Protonation Constants, Partition Coefficients, and Model Topologies". Journal of Chemical Information and Modeling 61 1 (2021): 335-346. http://dx.doi.org/10.1021/acs.jcim.0c01077.
    10.1021/acs.jcim.0c01077
  15. Borges-Araújo, Luis; Domingues, Marco; A.A. Fedorov, ; Nuno C. Santos; Manuel N. Melo; FERNANDES, FABIO. Corresponding author: FERNANDES, FABIO. "Acyl-chain saturation regulates the order of phosphatidylinositol 4,5-biphosphate nanodomains". Communications chemistry 4 1 (2021): 164. https://DOI.org/10.1038/s42004-021-00603-.
    Published • DOI:10.1038/s42004-021-00603-1
  16. Juanjuan Su; Siewert J. Marrink; Manuel N. Melo. "Localization Preference of Antimicrobial Peptides on Liquid-Disordered Membrane Domains". Frontiers in Cell and Developmental Biology, section Cellular Biochemistry (2020):
    Open access • Accepted
  17. Schroer, Carsten F. E.; Baldauf, Lucia; van Buren, Lennard; Wassenaar, Tsjerk A.; Melo, Manuel N.; Koenderink, Gijsje H.; Marrink, Siewert J.. "Charge-dependent interactions of monomeric and filamentous actin with lipid bilayers". Proceedings of the National Academy of Sciences 117 11 (2020): 5861-5872. http://dx.doi.org/10.1073/pnas.1914884117.
    10.1073/pnas.1914884117
  18. MELO, MANUEL. "Pitfalls of the Martini Model". Journal of Chemical Theory and Computation (2019): http://dx.doi.org/10.1021/acs.jctc.9b00473.
    10.1021/acs.jctc.9b00473
  19. MELO, MANUEL. "Self-assembly Stability Compromises the Efficacy of Tryptophan-Containing Designed Anti-measles Virus Peptides". Journal of Nanomedicine & Nanotechnology (2019): http://dx.doi.org/10.35248/2157-7439.19.10.528.
    10.35248/2157-7439.19.10.528
  20. Dadsena, Shashank; Bockelmann, Svenja; Mina, John G.M.; Hassan, Dina G.; Korneev, Sergei; Razzera, Guilherme; Jahn, Helene; et al. "Ceramides bind VDAC2 to trigger mitochondrial apoptosis". Nature Communications (2019): http://hdl.handle.net/10362/92533.
    https://doi.org/10.1038/s41467-019-09654-4
  21. Corradi, V.; Mendez-Villuendas, E.; Ingólfsson, H.I.; Gu, R.-X.; Siuda, I.; Melo, M.N.; Moussatova, A.; et al. "Lipid-Protein Interactions Are Unique Fingerprints for Membrane Proteins". ACS Central Science 4 6 (2018): 709-717. http://www.scopus.com/inward/record.url?eid=2-s2.0-85049133840&partnerID=MN8TOARS.
    10.1021/acscentsci.8b00143
  22. Su, J.; Thomas, A.S.; Grabietz, T.; Landgraf, C.; Volkmer, R.; Marrink, S.J.; Williams, C.; Melo, M.N.. "The N-terminal amphipathic helix of Pex11p self-interacts to induce membrane remodelling during peroxisome fission". Biochimica et Biophysica Acta - Biomembranes 1860 6 (2018): 1292-1300. http://www.scopus.com/inward/record.url?eid=2-s2.0-85043475518&partnerID=MN8TOARS.
    10.1016/j.bbamem.2018.02.029
  23. Figueira, Tiago Nascimento; Mendonça, Diogo A.; Gaspar, Diana; Melo, Manuel N.; Moscona, Anne; Porotto, Matteo; Castanho, Miguel A. R. B.; Veiga, Ana Salomé. "Structure-stability-function mechanistic links in the anti-measles virus action of Tocopherol-derivatized peptide nanoparticles". (2018): http://hdl.handle.net/10451/37690.
    10.1021/acsnano.8b01422
  24. Van Eerden, F.J.; Melo, M.N.; Frederix, P.W.J.M.; Marrink, S.J.. "Prediction of Thylakoid Lipid Binding Sites on Photosystem II". Biophysical Journal 113 12 (2017): 2669-2681. http://www.scopus.com/inward/record.url?eid=2-s2.0-85038395928&partnerID=MN8TOARS.
    10.1016/j.bpj.2017.09.039
  25. Van Eerden, F.J.; Melo, M.N.; Frederix, P.W.J.M.; Periole, X.; Marrink, S.J.. "Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex". Nature Communications 8 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85038408628&partnerID=MN8TOARS.
    10.1038/ncomms15214
  26. Melo, M.N.; Arnarez, C.; Sikkema, H.; Kumar, N.; Walko, M.; Berendsen, H.J.C.; Kocer, A.; Marrink, S.J.; Ingólfsson, H.I.. "High-Throughput Simulations Reveal Membrane-Mediated Effects of Alcohols on MscL Gating". Journal of the American Chemical Society 139 7 (2017): 2664-2671. http://www.scopus.com/inward/record.url?eid=2-s2.0-85013499843&partnerID=MN8TOARS.
    10.1021/jacs.6b11091
  27. Zavadlav, J.; Podgornik, R.; Melo, M.N.; Marrink, S.J.; Praprotnik, M.. "Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution". European Physical Journal: Special Topics 225 8-9 (2016): 1595-1607. http://www.scopus.com/inward/record.url?eid=2-s2.0-84978786373&partnerID=MN8TOARS.
    10.1140/epjst/e2016-60117-8
  28. Smeets, C.J.L.M.; Zmorzynska, J.; Melo, M.N.; Stargardt, A.; Dooley, C.; Bakalkin, G.; McLaughlin, J.; et al. "Altered secondary structure of Dynorphin A associates with loss of opioid signalling and NMDA-mediated excitotoxicity in SCA23". Human Molecular Genetics 25 13 (2016): 2728-2737. http://www.scopus.com/inward/record.url?eid=2-s2.0-85016079961&partnerID=MN8TOARS.
    10.1093/hmg/ddw130
  29. Arnarez, C.; Uusitalo, J.J.; Masman, M.F.; Ingólfsson, H.I.; De Jong, D.H.; Melo, M.N.; Periole, X.; De Vries, A.H.; Marrink, S.J.. "Dry martini, a coarse-grained force field for lipid membrane simulations with implicit solvent". Journal of Chemical Theory and Computation 11 1 (2015): 260-275. http://www.scopus.com/inward/record.url?eid=2-s2.0-84921411802&partnerID=MN8TOARS.
    10.1021/ct500477k
  30. Melo, M.N.; Ingólfsson, H.I.; Marrink, S.J.. "Parameters for Martini sterols and hopanoids based on a virtual-site description". Journal of Chemical Physics 143 24 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84952332821&partnerID=MN8TOARS.
    10.1063/1.4937783
  31. Zavadlav, J.; Melo, M.N.; Marrink, S.J.; Praprotnik, M.. "Adaptive resolution simulation of polarizable supramolecular coarse-grained water models". Journal of Chemical Physics 142 24 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84934294910&partnerID=MN8TOARS.
    10.1063/1.4923008
  32. Goga, N.; Melo, M.N.; Rzepiela, A.J.; De Vries, A.H.; Hadar, A.; Marrink, S.J.; Berendsen, H.J.C.. "Benchmark of schemes for multiscale molecular dynamics simulations". Journal of Chemical Theory and Computation 11 4 (2015): 1389-1398. http://www.scopus.com/inward/record.url?eid=2-s2.0-84927767282&partnerID=MN8TOARS.
    10.1021/ct501102b
  33. Uytterhoeven, V.; Lauwers, E.; Maes, I.; Miskiewicz, K.; Melo, M.N.; Swerts, J.; Kuenen, S.; et al. "Hsc70-4 Deforms Membranes to Promote Synaptic Protein Turnover by Endosomal Microautophagy". Neuron 88 4 (2015): 735-748. http://www.scopus.com/inward/record.url?eid=2-s2.0-84959871737&partnerID=MN8TOARS.
    10.1016/j.neuron.2015.10.012
  34. Zavadlav, J.; Melo, M.N.; Marrink, S.J.; Praprotnik, M.. "Adaptive resolution simulation of an atomistic protein in MARTINI water". Journal of Chemical Physics 140 5 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84902200025&partnerID=MN8TOARS.
    10.1063/1.4863329
  35. Zavadlav, J.; Melo, M.N.; Cunha, A.V.; De Vries, A.H.; Marrink, S.J.; Praprotnik, M.. "Adaptive resolution simulation of MARTINI solvents". Journal of Chemical Theory and Computation 10 6 (2014): 2591-2598. http://www.scopus.com/inward/record.url?eid=2-s2.0-84902176050&partnerID=MN8TOARS.
    10.1021/ct5001523
  36. Ingólfsson, H.I.; Melo, M.N.; Van Eerden, F.J.; Arnarez, C.; Lopez, C.A.; Wassenaar, T.A.; Periole, X.; et al. "Lipid organization of the plasma membrane". Journal of the American Chemical Society 136 41 (2014): 14554-14559. http://www.scopus.com/inward/record.url?eid=2-s2.0-84908374604&partnerID=MN8TOARS.
    10.1021/ja507832e
  37. Serrano, I.D.; Freire, J.M.; Carvalho, M.V.; Neves, M.; Melo, M.N.; Castanho, M.A.R.B.. "The mechanisms and quantification of the selective permeability in transport across biological barriers: The example of kyotorphin". Mini-Reviews in Medicinal Chemistry 14 2 (2014): 99-110. http://www.scopus.com/inward/record.url?eid=2-s2.0-84894043648&partnerID=MN8TOARS.
    10.2174/1389557514666140123130058
  38. Van Hell, A.J.; Melo, M.N.; Van Blitterswijk, W.J.; Gueth, D.M.; Braumuller, T.M.; Pedrosa, L.R.C.; Song, J.-Y.; et al. "Defined lipid analogues induce transient channels to facilitate drug-membrane traversal and circumvent cancer therapy resistance". Scientific Reports 3 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84902941080&partnerID=MN8TOARS.
    10.1038/srep01949
  39. Cruz, V.L.; Ramos, J.; Melo, M.N.; Martinez-Salazar, J.. "Bacteriocin AS-48 binding to model membranes and pore formation as revealed by coarse-grained simulations". Biochimica et Biophysica Acta - Biomembranes 1828 11 (2013): 2524-2531. http://www.scopus.com/inward/record.url?eid=2-s2.0-84882696543&partnerID=MN8TOARS.
    10.1016/j.bbamem.2013.05.036
  40. Melo, M.N.; Castanho, M.A.R.B.; Melo, Manuel N.; Castanho, Miguel A. R. B.. "The mechanism of action of antimicrobial peptides: Lipid vesicles vs. bacteria". Frontiers in Immunology 3 AUG (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84874199480&partnerID=MN8TOARS.
    10.3389/fimmu.2012.00236
  41. Melo, M.N.; Ferre, R.; Feliu, L.; Bardají, E.; Planas, M.; Castanho, M.A.R.B.. "Prediction of antibacterial activity from physicochemical properties of antimicrobial peptides". PLoS ONE 6 12 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-83355168944&partnerID=MN8TOARS.
    10.1371/journal.pone.0028549
  42. Freire, João M.; Domingues, Marco M.; Matos, Joana; Melo, Manuel N.; Veiga, Ana Salomé; Santos, Nuno C.; Castanho, Miguel A. R. B.; et al. "Using zeta-potential measurements to quantify peptide partition to lipid membranes". European Biophysics Journal 40 4 (2011): 481-487. http://dx.doi.org/10.1007/s00249-010-0661-4.
    http://dx.doi.org/10.1007/s00249-010-0661-4
  43. Alves, C.S.; Melo, M.N.; Franquelim, H.G.; Ferre, R.; Planas, M.; Feliu, L.; Bardají, E.; et al. "Escherichia coli cell surface perturbation and disruption induced by antimicrobial peptides BP100 and pepR". Journal of Biological Chemistry 285 36 (2010): 27536-27544. http://www.scopus.com/inward/record.url?eid=2-s2.0-77956238793&partnerID=MN8TOARS.
    10.1074/jbc.M110.130955
  44. Ribeiro, M.M.B.; Melo, M.N.; Serrano, I.D.; Santos, N.C.; Castanho, M.A.R.B.; Ribeiro, Marta M. B.; Melo, Manuel N.; et al. "Drug-lipid interaction evaluation: Why a 19th century solution?". Trends in Pharmacological Sciences 31 10 (2010): 449-454. http://www.scopus.com/inward/record.url?eid=2-s2.0-77956909526&partnerID=MN8TOARS.
    10.1016/j.tips.2010.06.007
  45. Ferre, R.; Melo, M.N.; Correia, A.D.; Feliu, L.; Bardaji, E.; Planas, M.; Castanho, M.; et al. "Synergistic effects of the membrane actions of cecropin-melittin antimicrobial hybrid peptide BP100". Biophysical Journal 96 5 (2009): 1815-1827. http://www.scopus.com/inward/record.url?eid=2-s2.0-65549119292&partnerID=MN8TOARS.
    10.1016/j.bpj.2008.11.053
  46. Melo, M.N.; Ferre, R.; Castanho, M.A.R.B.. "Antimicrobial peptides: Linking partition, activity and high membrane-bound concentrations". Nature Reviews Microbiology 7 3 (2009): 245-250. http://www.scopus.com/inward/record.url?eid=2-s2.0-60749118913&partnerID=MN8TOARS.
    10.1038/nrmicro2095
  47. Melo, M.N.; Sousa, F.J.R.; Carneiro, F.A.; Castanho, M.A.R.B.; Valente, A.P.; Almeida, F.C.L.; Da Poian, A.T.; et al. "Interaction of the Dengue Virus Fusion Peptide with Membranes Assessed by NMR: The Essential Role of the Envelope Protein Trp101 for Membrane Fusion". Journal of Molecular Biology 392 3 (2009): 736-746. http://www.scopus.com/inward/record.url?eid=2-s2.0-69549116106&partnerID=MN8TOARS.
    10.1016/j.jmb.2009.07.035
  48. Stauffer, F.; Melo, M.N.; Carneiro, F.A.; Sousa, F.J.R.; Juliano, M.A.; Juliano, L.; Mohana-Borges, R.; Da Poian, A.T.; Castanho, M.A.R.B.. "Interaction between dengue virus fusion peptide and lipid bilayers depends on peptide clustering". Molecular Membrane Biology 25 2 (2008): 128-138. http://www.scopus.com/inward/record.url?eid=2-s2.0-39849096708&partnerID=MN8TOARS.
    10.1080/09687680701633091
  49. Gutierrez, A.L.S.; Farage, L.; Melo, M.N.; Mohana-Borges, R.S.; Guerardel, Y.; Coddeville, B.; Mendonça-Previato, L.. "Characterization of glycoinositolphosphoryl ceramide structure mutant strains of Cryptococcus neoformans". Glycobiology 17 6 (2007): http://www.scopus.com/inward/record.url?eid=2-s2.0-34447297313&partnerID=MN8TOARS.
    10.1093/glycob/cwm030
  50. Henriques, S.T.; Melo, M.N.; Castanho, M.A.R.B.. "How to address CPP and AMP translocation? Methods to detect and quantify peptide internalization in vitro and in vivo (review)". Molecular Membrane Biology 24 3 (2007): 173-185. http://www.scopus.com/inward/record.url?eid=2-s2.0-34249036121&partnerID=MN8TOARS.
    10.1080/09687860601102476
  51. Melo, M.N.; Castanho, M.A.R.B.. "Omiganan interaction with bacterial membranes and cell wall models. Assigning a biological role to saturation". Biochimica et Biophysica Acta - Biomembranes 1768 5 (2007): 1277-1290. http://www.scopus.com/inward/record.url?eid=2-s2.0-34047249400&partnerID=MN8TOARS.
    10.1016/j.bbamem.2007.02.005
  52. Melo, M.N.; Dugourd, D.; Castanho, M.A.. "Omiganan pentahydrochloride in the front line of clinical applications of antimicrobial peptides.". Recent patents on anti-infective drug discovery 1 2 (2006): 201-207. http://www.scopus.com/inward/record.url?eid=2-s2.0-33749376228&partnerID=MN8TOARS.
    10.2174/157489106777452638
  53. Henriques, S.T.; Melo, M.N.; Castanho, M.A.R.B.. "Cell-penetrating peptides and antimicrobial peptides: How different are they?". Biochemical Journal 399 1 (2006): 1-7. http://www.scopus.com/inward/record.url?eid=2-s2.0-33749385780&partnerID=MN8TOARS.
    10.1042/BJ20061100
Online resource
  1. Gaspar, Catarina J.; Joana C Martins; Manuel N. Melo; Tiago N Cordeiro; Adrain, Colin; Domingos, Pedro. Corresponding author: Domingos, Pedro. Xport-A functions as a chaperone by stabilizing the first 5 transmembrane domains of Rhodopsin-1. 2022. https://www.biorxiv.org/content/10.1101/2022.04.01.486763v1.
    https://doi.org/10.1101/2022.04.01.486763
Preprint
  1. Paulo C. T. Souza; Luis P. Borges Araujo; Chris Brasnett; Rodrigo A. Moreira; Fabian Grunewald; Peter Park; Liguo Wang; et al. "GoMartini 3: From large conformational changes in proteins to environmental bias corrections". 2024. https://doi.org/10.1101/2024.04.15.589479.
    10.1101/2024.04.15.589479
  2. Catarina J Gaspar; Joana C Martins; Manuel N Melo; Tiago N Cordeiro; Colin Adrain; Pedro M Domingos. "Xport-A functions as a chaperone by stabilizing the first 5 transmembrane domains of Rhodopsin-1". 2022. https://doi.org/10.1101/2022.04.01.486763.
    10.1101/2022.04.01.486763
  3. J. Karl Spinti; Fernando Neiva Nunes; Manuel Nuno Melo. "Room for Improvement in the Initial Martini 3 Parameterization of Peptide Interactions". 2022. https://doi.org/10.26434/chemrxiv-2022-wgz1j.
    10.26434/chemrxiv-2022-wgz1j
  4. Luis Borges-Araújo; Paulo Souza; Fábio Fernandes; Manuel N. Melo. "Improved Parameterization of Phosphatidylinositide Lipid Headgroups for the Martini 3 Coarse Grain Force Field". 2021. https://doi.org/10.26434/chemrxiv.14759991.v2.
    10.26434/chemrxiv.14759991.v2
  5. Valério, Mariana; Borges-Araújo, Luís; Melo, Manuel N.; Lousa, Diana; Soares, Cláudio M.. "SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility". 2021. http://dx.doi.org/10.1101/2021.11.30.470470.
    10.1101/2021.11.30.470470
  6. Riccardo Alessandri; Paulo C. T. Souza; Sebastian Thallmair; Manuel N. Melo; Alex H. de Vries; Siewert-Jan Marrink. "Pitfalls of the Martini Model". 2019. https://doi.org/10.26434/chemrxiv.8113172.v1.
    10.26434/chemrxiv.8113172.v1
Thesis / Dissertation
  1. Melo, Manuel Nuno, 1982-. "A study on the mode of action of clinically relevant antimicrobial peptides". PhD, 2010. http://hdl.handle.net/10451/1881.

Other

Other output
  1. MDAnalysis. A Python package for the analysis of molecular dynamics simulations.. 2012. MELO, MANUEL. https://www.mdanalysis.org/.
  2. MDreader. A package to boost MD data analysis with parallelization. 2012. MELO, MANUEL. https://github.com/mnmelo/MDreader.
Distinctions

Other distinction

2018 FCT Scientific Employment Stimulus Fellow
Fundação para a Ciência e a Tecnologia, Portugal
2013 NWO VENI Individual Postdoctoral Fellowship
Nederlandse Organisatie voor Wetenschappelijk Onderzoek, Netherlands
2010 Marie Sklodowska-Curie Individual Intra-European Postdoctoral Fellowship
EU Framework Programme for Research and Innovation Marie Sklodowska-Curie Actions, Belgium