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 2007-200848. Carvalho, A. T. P., Fernandes, P. A., & Ramos, M. J. (2007). The excision mechanism in reverse transcriptase: Pyrophosphate leaving and fingers opening are uncoupled events with the analogues AZT and d4T. Journal of Physical Chemistry B, 111(41), 12032-12039. doi:10.1021/jp0746594
49. Carvalho, A. T. P., Fernandes, P. A., & Ramos, M. J. (2007). Parameterization of AZT - A widely used nucleoside inhibitor of HIV-1 reverse transcriptase. International Journal of Quantum Chemistry, 107(2), 292-298. doi:10.1002/qua.21192
50. Cerqueira, N., Fernandes, P. A., & Ramos, M. J. (2007). Ribonucleotide reductase: A critical enzyme for cancer chemotherapy and antiviral agents. Recent Patents on Anti-Cancer Drug Discovery, 2(1), 11-29.
51. Cerqueira, N., Fernandes, P. A., & Ramos, M. L. (2007). Understanding ribonucleotide reductase inactivation by gemcitabine. Chemistry-a European Journal, 13(30), 8507-8515. doi:10.1002/chem.200700260
52. Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2007). Hot spots-A review of the protein-protein interface determinant amino-acid residues. Proteins-Structure Function and Bioinformatics, 68(4), 803-812. doi:10.1002/prot.21396
53. Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2007). Backbone importance for protein-protein binding. Journal of Chemical Theory and Computation, 3(3), 885-893. doi:10.1021/ct6003824
54. Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2007). Hot spot occlusion from bulk water: A comprehensive study of the complex between the lysozyme HEL and the antibody FVD1.3. Journal of Physical Chemistry B, 111(10), 2697-2706. doi:10.1021/jp067096p
55. Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2007). Vascular endothelial growth factor (VEGF) inhibition - A critical review. Anti-Cancer Agents in Medicinal Chemistry, 7(2), 223-245.
56. Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2007). Hot spot computational identification: Application to the complex formed between the hen egg white lysozyme (HEL) and the antibody HyHEL-10. International Journal of Quantum Chemistry, 107(2), 299-310. doi:10.1002/qua.21193
57. Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2007). Computational alanine scanning mutagenesis - An improved methodological approach. Journal of Computational Chemistry, 28(3), 644-654. doi:10.1002/jcc.20566
58. Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2007). Unravelling Hot Spots: a comprehensive computational mutagenesis study. Theoretical Chemistry Accounts, 117(1), 99-113. doi:10.1007/s00214-006-0151-z
59. Perez, M. A. S., Fernandes, P. A., & Ramos, M. J. (2007). Drug design: New inhibitors for HIV-1 protease based on Nelfinavir as lead. Journal of Molecular Graphics & Modelling, 26(3), 634-642. doi:10.1016/j.jmgm.2007.03.009
60. Sousa, S. F., Fernandes, P. A., & Ramos, M. J. (2007). General performance of density functionals. Journal of Physical Chemistry A, 111(42), 10439-10452. doi:10.1021/jp0734474
61. Sousa, S. F., Fernandes, P. A., & Ramos, M. J. (2007). Comparative assessment of theoretical methods for the determination of geometrical properties in biological zinc complexes. Journal of Physical Chemistry B, 111(30), 9146-9152. doi:10.1021/jp072538y
62. Sousa, S. F., Fernandes, P. A., & Ramos, M. J. (2007). Theoretical studies on farnesyltransferase: Evidence for thioether product coordination to the active-site zinc sphere. Journal of Computational Chemistry, 28(7), 1160-1168. doi:10.1002/jcc.20577
63. Sousa, S. F., Fernandes, P. A., & Ramos, M. J. (2007). The carboxylate shift in zinc enzymes: A computational study. Journal of the American Chemical Society, 129(5), 1378-1385. doi:10.1021/ja067103n
64. Sousa, S. F., Fernandes, P. A., & Ramos, M. J. (2007). Theoretical studies on farnesyltransferase: The distances paradox explained. Proteins-Structure Function and Bioinformatics, 66(1), 205-218. doi:10.1002/prot.21219
65. Sousa, S. F., Fernandes, P. A., & Ramos, M. J. (2007). Effective tailor-made force field parameterization of the several Zn coordination environments in the puzzling FTase enzyme: opening the door to the full understanding of its elusive catalytic mechanism. Theoretical Chemistry Accounts, 117(1), 171-181. doi:10.1007/s00214-006-0170-9
66. Tamames, B., Sousa, S. F., Tamames, J., Fernandes, P. A., & Ramos, M. J. (2007). Analysis of zinc-ligand bond lengths in metalloproteins: Trends and patterns. Proteins-Structure Function and Bioinformatics, 69(3), 466-475. doi:10.1002/prot.21536
67. Bras, N. F., Cerqueira, N., Fernandes, P. A., & Ramos, M. J. (2008). Carbohydrate-binding modules from family 11: Understanding the binding mode of polysaccharides. International Journal of Quantum Chemistry, 108(11), 2030-2040. doi:10.1002/qua.21755
68. Bras, N. F., Moura-Tamames, S. A., Fernandes, P. A., & Ramos, M. J. (2008). Mechanistic Studies on the Formation of Glycosidase-Substrate and Glycosidase-Inhibitor Covalent Intermediates. Journal of Computational Chemistry, 29(15), 2565-2574. doi:10.1002/jcc.21013
69. Carvalho, A. T. P., Swart, M., van Stralen, J. N. P., Fernandes, P. A., Ramos, M. J., & Bickelhaupt, F. M. (2008). Mechanism of thioredoxin-catalyzed disulfide reduction. Activation of the buried thiol and role of the variable active-site residues. Journal of Physical Chemistry B, 112(8), 2511-2523. doi:10.1021/jp7104665
70. Dourado, D., Fernandes, P. A., Mannervik, B., & Ramos, M. J. (2008). Glutathione Transferase: New Model for Glutathione Activation. Chemistry-a European Journal, 14(31), 9591-9598. doi:10.1002/chem.200800946
71. Dourado, D., Fernandes, P. A., & Ramos, M. J. (2008). Mammalian cytosolic glutathione transferases. Current Protein & Peptide Science, 9(4), 325-337. doi:10.2174/138920308785132677
72. Marques, A. T., Antunes, A., Fernandes, P. A., & Ramos, M. J. (2008). Computational optimization of AG18051 inhibitor for amyloid-beta binding alcohol dehydrogenase enzyme. International Journal of Quantum Chemistry, 108(11), 1982-1991. doi:10.1002/qua.21716
73. Marques, A. T., Fernandes, P. A., & Ramos, M. J. (2008). Molecular dynamics simulations of the amyloid-beta binding alcohol dehydrogenase (ABAD) enzyme. Bioorganic & Medicinal Chemistry, 16(21), 9511-9518. doi:10.1016/j.bmc.2008.09.043
74. Martins, S., Ramos, M. J., & Fernandes, P. A. (2008). The current status of the NNRTI family of antiretrovirals used in the HAART regime against HIV infection. Current Medicinal Chemistry, 15(11), 1083-1095. doi:10.2174/092986708784221467
75. Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2008). Protein-protein recognition: a computational mutagenesis study of the MDM2-P53 complex. Theoretical Chemistry Accounts, 120(4-6), 533-542. doi:10.1007/s00214-008-0432-9
76. Ramos, M. J., & Fernandes, P. A. (2008). Computational enzymatic catalysis. Accounts of Chemical Research, 41(6), 689-698. doi:10.1021/ar7001045
77. Sousa, S. F., Fernandes, P. A., & Ramos, M. J. (2008). Molecular dynamics analysis of farnesyltransferase: A closer look into the amino acid behavior. International Journal of Quantum Chemistry, 108(11), 1939-1950. doi:10.1002/qua.21713
78. Sousa, S. F., Fernandes, P. A., & Ramos, M. J. (2008). Enzyme flexibility and the catalytic mechanism of farnesyltransferase: Targeting the relation. Journal of Physical Chemistry B, 112(29), 8681-8691. doi:10.1021/jp711214j
79. Sousa, S. F., Fernandes, P. A., & Ramos, M. J. (2008). Farnesyltransferase inhibitors: A detailed chemical view on an elusive biological problem. Current Medicinal Chemistry, 15(15), 1478-1492. doi:10.2174/092986708784638825
80. Viegas, A., Bras, N. F., Cerqueira, N., Fernandes, P. A., Prates, J. A. M., Fontes, C., . . . Cabrita, E. J. (2008). Molecular determinants of ligand specificity in family 11 carbohydrate binding modules - an NMR, X-ray crystallography and computational chemistry approach. Febs Journal, 275(10), 2524-2535. doi:10.1111/j.1742-4658.2008.06401.x