Selected Publications
Please find below a selection of my publications, divided by date and updated at 14/Jun/2019
You can also find my publications at Google Scholar, in the ISI Web of Knowledge or in ORCID.
2018-2020| 2015-2017 | 2013-2014 | 2011-2012 | 2009-2010 | 2007-2008 | 2005-2006 | 2003-2004 | Before 2003|
Publications 2005-200621. Carvalho, ATP; Fernandes, PA; Ramos, MJ Insights on resistance to reverse transcriptase: The different patterns of interaction of the nucleoside reverse transcriptase inhibitors in the deoxyribonucleotide triphosphate binding site relative to the normal substrate, J. Med. Chem., 2006, 49, 7675.
22. Moreira, IS; Fernandes, PA; Ramos, MJ Hot spot computational identification: Application to the complex formed between the hen egg white lysozyme (HEL) and the antibody HyHEL-10, Int. J. Quantum Chem., 2006, 107, 299.
23. Carvalho, ATP; Fernandes, PA; Ramos, MJ Molecular Dynamics Model Of Unliganded HIV-1 Reverse Transcriptase, Med. Chem., 2006, 2, 491.
24. Ramos, MJ; Fernandes, PA Atomic-Level Rational Drug Design, Curr. Comput.-Aided Drug Design, 2006, 3, 325.
25. Cerqueira, NMFSA; Fernandes, PA; Ramos, MJ Enzyme ribonucleotide reductase: Unraveling an enigmatic paradigm of enzyme inhibition by furanone derivatives, J. Phys. Chem. B, 2006, 110, 21272.
26. Marques, AT; Antunes, A; Fernandes, PA; Ramos, MJ Comparative evolutionary genomics of the HADH2 gene encoding A beta-binding alcohol dehydrogenase/17 beta-hydroxysteroid dehydrogenase type 10 (ABAD/HSD10), BMC Genomics, 2006, 7: Art. No. 202.
27. Sousa, SF; Fernandes, PA; Ramos, MJ Protein-ligand docking: Current status and future challenges, Proteins, 2006, 65, 15.
28. Branco, RJF; Fernandes, PA; Ramos, MJ Molecular dynamics simulations of the enzyme Cu, Zn superoxide dismutase, J. Phys. Chem. B, 2006, 110, 16754.
29. Fernandes, PA; Araujo, MLAC; Barbosa, AJM; Alves, CN; Ferreira, ZQ; Gonzalez, CRN; Lima, CFRAC; Loureiro, SIE; Magalhaes, JMT; Maia, FC; Moura, SA; Peredo, EMM; Perez, MAS; Rodrigues, TAQ; Pessoa, AM; da Silva, CAM; da Silva, JPA; Ramos, MJ Lead optimisation: Improving the affinity of the antiretrovirals Nelfinavir and Amprenavir for HIV-1 protease, Lett. Drug Design Discov., 2006, 3, 383.
30. Carvalho, AP; Fernandes, PA; Ramos, MJ Similarities and differences in the thioredoxin superfamily, Progress Biophys Mol. Biol., 2006, 91, 229.
31. Moreira, IS; Fernandes, PA; Ramos, MJ Detailed microscopic study of the full ZipA : FtsZ interface, Proteins, 2006, 63, 811.
32. Moreira, IS; Fernandes, PA; Ramos, MJ Unraveling the importance of protein-protein interaction: Application of a computational alanine-scanning mutagenesis to the study of the IgG1 streptococcal protein G (C2 fragment) complex, J. Phys. Chem. B, 2006, 110, 10962.
33. Carvalho, AP; Fernandes, PA; Ramos, MJ Molecular insights into the mechanisms of HIV-1 reverse transcriptase resistance to nucleoside analogs, Mini-Rev. Med. Chem., 2006, 6, 549.
34. Carvalho, ATP; Fernandes, PA; Ramos, MJ Determination of the Delta pKa between the active site cysteines of thioredoxin and DsbA, J. Comput. Chem., 2006, 27, 966.
35. Carvalho, ATP; Fernandes, PA; Ramos, MJ Theoretical study of the unusual protonation properties of the active site cysteines in thioredoxin, J. Phys. Chem. B, 2006, 110, 5758.
36. Cerqueira, NMFSA; Fernandes, PA; Eriksson, LA; Ramos, MJ Dehydration of ribonucleotides catalyzed by ribonucleotide reductase: The role of the enzyme, Biophys. J., 2006, 90, 2109.
37. Branco, RJF; Fernandes, PA; Ramos, MJ Cu, Zn Superoxide dismutase: distorted active site binds substrate without significant energetic cost, Theor. Chem. Acc., 2006, 115, 27.
38. Tamames, B; Fernandes, PA; Ramos, MJ Catalysis and Inhibition of HIV-1 Protease, Curr. Bioactive Comp., 2006, 2, 243.
39. Pereira, S; Cerqueira, NMFSA; Fernandes, PA; Ramos, MJ Computational studies on class I ribonucleotide reductase: Understanding the mechanisms of action and inhibition of a cornerstone enzyme for the treatment of cancer, Eur. Biophys. J. Biophys. Lett., 2006, 35, 125.
40. Moreira, IS; Fernandes, PA; Ramos, MJ Accuracy of the numerical solution of the Poisson-Boltzmann equation, THEOCHEM, 2005, 729, 11.
41. Sousa, SF; Fernandes, PA; Ramos, MJ Farnesyltransferase: Theoretical studies on peptide substrate entrance thiol or thiolate coordination? THEOCHEM, 2005, 729, 125
42. Branco, RJF; Fernandes, PA; Ramos, MJ Density-functional calculations of the Cu, Zn superoxide dismutase redox potential: The influence of active site distortion, THEOCHEM, 2005, 729, 141.
43. Fernandes, PA; Maia, ARR; Almeida, AAS; Silva, BFB; Ribeiro, CMS; Ribeiro, CFB; Ribeiro, DSM; Fonseca, DAP; Henriques, ES; Cunha, EMS; Maia, FRNC; Pereira, JAA; Pacheco, JPG; Ferreira, JAAD; Matos, LRC; Pinto, MABP; Borges, MCS; Magalhaes, PJCR; Teixeira, PFRD; Veloso, PNBC; Ferreira, RJF; Gomes, SS; Barros, TF; Selao, TSJT; Pande, V; Fernandes, VMMC; Ramos, MJ New designs for inhibitors of the NF-kappa B: DNA binding, Theor. Chem. Acc., 2005, 113, 197.
44. Cerqueira, NMFSA; Pereira, S; Fernandes, PA; Ramos, MJ Overview of ribonucleotide reductase inhibitors: An appealing target in anti-tumour therapy, Curr. Med Chem., 2005, 12, 1283.
45. Pereira, S; Fernandes, PA; Ramos, MJ Theoretical study on the inhibition of ribonucleotide reductase by 2 '-mercapto-2 '-deoxyribonucleoside-5 '-diphosphates, J. Am. Chem. Soc., 2005, 127, 5174.
46. Sousa, SF; Fernandes, PA; Ramos, MJ Unraveling the mechanism of the farnesyltransferase enzyme, J. Biol. Inorg. Chem., 2005, 10, 3.
47. Sousa, SF; Fernandes, PA; Ramos, MJ Farnesyltransferase - New insights into the zinc-coordination sphere paradigm: Evidence for a carboxylate-shift mechanism, Biophys. J., 2005, 88, 483.