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 2009-201081. Bras, N. F., Fernandes, P. A., & Ramos, M. J. (2009). Docking and molecular dynamics studies on the stereoselectivity in the enzymatic synthesis of carbohydrates. Theoretical Chemistry Accounts, 122(5-6), 283-296. doi:10.1007/s00214-009-0507-2
82. Carvalho, A. T. P., Fernandes, P. A., Swart, M., van Stralen, J. N. P., Bickelhaupt, F. M., & Ramos, M. J. (2009). Role of the Variable Active Site Residues in the Function of Thioredoxin Family Oxidoreductases. Journal of Computational Chemistry, 30(5), 710-724. doi:10.1002/jcc.21086
83. Cerqueira, N., Bras, N. F., Fernandes, P. A., & Ramos, M. J. (2009). MADAMM: A multistaged docking with an automated molecular modeling protocol. Proteins-Structure Function and Bioinformatics, 74(1), 192-206. doi:10.1002/prot.22146
84. Dourado, D., Fernandes, P. A., & Ramos, M. J. (2009). Glutathione transferase A1-1: catalytic role of water. Theoretical Chemistry Accounts, 124(1-2), 71-83. doi:10.1007/s00214-009-0582-4
85. Marques, A. T., Fernandes, P. A., & Ramos, M. J. (2009). ABAD: A Potential Therapeutic Target for A beta-Induced Mitochondrial Dysfunction in Alzheimer's Disease. Mini-Reviews in Medicinal Chemistry, 9(8), 1002-1008. doi:10.2174/138955709788681627
86. Moura-Tamames, S., Ramos, M. J., & Fernades, P. A. (2009). Modelling beta-1,3-Exoglucanase- saccharide interactions: structure of the enzyme-substrate complex and enzyme binding to the cell wall. Febs Journal, 276, 156-157.
87. Moura-Tamames, S. A., Ramos, M. J., & Fernades, P. A. (2009). Exploring beta-1,3-Exoglucanase-polysaccharide interactions: molecular dynamics of the enzyme-substrate complex with or without a polysaccharide ligand bound in the flexible enzyme loops. Febs Journal, 276, 156-156.
88. Moura-Tamames, S. A., Ramos, M. J., & Fernandes, P. A. (2009). Modelling beta-1,3-exoglucanase-saccharide interactions: Structure of the enzyme-substrate complex and enzyme binding to the cell wall. Journal of Molecular Graphics & Modelling, 27(8), 908-920. doi:10.1016/j.jmgm.2009.01.007
89. Sousa, S. F., Carvalho, E. S., Ferreira, D. M., Tavares, I. S., Fernandes, P. A., Ramos, M. J., & Gomes, J. (2009). Comparative Analysis of the Performance of Commonly Available Density Functionals in the Determination of Geometrical Parameters for Zinc Complexes. Journal of Computational Chemistry, 30(16), 2752-2763. doi:10.1002/jcc.21304
90. Sousa, S. F., Fernandes, P. A., & Ramos, M. J. (2009). Gas-Phase Geometry Optimization of Biological Molecules as a Reasonable Alternative to a Continuum Environment Description: Fact, Myth, or Fiction? Journal of Physical Chemistry A, 113(52), 14231-14236. doi:10.1021/jp902213t
91. Sousa, S. F., Fernandes, P. A., & Ramos, M. J. (2009). Molecular dynamics simulations on the critical states of the farnesyltransferase enzyme. Bioorganic & Medicinal Chemistry, 17(9), 3369-3378. doi:10.1016/j.bmc.2009.03.055
92. Sousa, S. F., Fernandes, P. A., & Ramos, M. J. (2009). The Search for the Mechanism of the Reaction Catalyzed by Farnesyltransferase. Chemistry-a European Journal, 15(17), 4243-4247. doi:10.1002/chem.200802745
93. Sousa, S. F., Lopes, A. B., Fernandes, P. A., & Ramos, M. J. (2009). The Zinc proteome: a tale of stability and functionality. Dalton Transactions(38), 7946-7956. doi:10.1039/b904404c
94. Tamames, B., Fernandes, P. A., & Ramos, M. J. (2009). HIV-1 Protease: a computational mutagenesis analysis of the monomers interface. Febs Journal, 276, 167-167.
95. Bras, N. F., Fernandes, P. A., & Ramos, M. J. (2010). QM/MM Studies on the beta-Galactosidase Catalytic Mechanism: Hydrolysis and Transglycosylation Reactions. Journal of Chemical Theory and Computation, 6(2), 421-433. doi:10.1021/ct900530f
96. Bras, N. F., Goncalves, R., Fernandes, P. A., Mateus, N., Ramos, M. J., & de Freitas, V. (2010). Understanding the Binding of Procyanidins to Pancreatic Elastase by Experimental and Computational Methods. Biochemistry, 49(25), 5097-5108. doi:10.1021/bi100410q
97. Bras, N. F., Goncalves, R., Mateus, N., Fernandes, P. A., Ramos, M. J., & Do Freitas, V. (2010). Inhibition of Pancreatic Elastase by Polyphenolic Compounds. Journal of Agricultural and Food Chemistry, 58(19), 10668-10676. doi:10.1021/jf1017934
98. Bras, N. F., Ramos, M. J., & Fernandes, P. A. (2010). DFT studies on the beta-glycosidase catalytic mechanism: The deglycosylation step. Journal of Molecular Structure-Theochem, 946(1-3), 125-133. doi:10.1016/j.theochem.2009.08.039
99. Dourado, D., Fernandes, P. A., Mannervik, B., & Ramos, M. J. (2010). Glutathione Transferase A1-1: Catalytic Importance of Arginine 15. Journal of Physical Chemistry B, 114(4), 1690-1697. doi:10.1021/jp908251z
100. Dourado, D., Fernandes, P. A., & Ramos, M. J. (2010). Glutathione Transferase Classes Alpha, Pi, and Mu: GSH Activation Mechanism. Journal of Physical Chemistry B, 114(40), 12972-12980. doi:10.1021/jp1053875
101. Marques, A. T., Fernandes, P. A., & Ramos, M. J. (2010). Structural Analysis of ABAD Point Mutations Causing 2-Methyl-3-hydroxylbutyryl-coA Deficiency. International Journal of Quantum Chemistry, 110(1), 148-160. doi:10.1002/qua.22091
102. Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2010). Protein-Protein Docking Dealing With the Unknown. Journal of Computational Chemistry, 31(2), 317-342. doi:10.1002/jcc.21276
103. Perez, M. A. S., Cerqueira, N., Fernandes, P. A., & Ramos, M. J. (2010). Ribonucleotide Reductase: A Mechanistic Portrait of Substrate Analogues Inhibitors. Current Medicinal Chemistry, 17(26), 2854-2872. doi:10.2174/092986710792065054
104. Perez, M. A. S., Fernandes, P. A., & Ramos, M. J. (2010). Understanding the Mechanism for Ribonucleotide Reductase Inactivation by 2 '-Deoxy-2 '-methylenecytidine-5 '-diphosphate. Journal of Chemical Theory and Computation, 6(9), 2770-2781. doi:10.1021/ct1002175
105. Perez, M. A. S., Fernandes, P. A., & Ramos, M. J. (2010). Substrate Recognition in HIV-1 Protease: A Computational Study. Journal of Physical Chemistry B, 114(7), 2525-2532. doi:10.1021/jp910958u
106. Ribeiro, A. J. M., Ramos, M. J., & Fernandes, P. A. (2010). Benchmarking of DFT Functionals for the Hydrolysis of Phosphodiester Bonds. Journal of Chemical Theory and Computation, 6(8), 2281-2292. doi:10.1021/ct900649e
107. Sousa, S. F., Cerqueira, N., Fernandes, P. A., & Ramos, M. J. (2010). Virtual Screening in Drug Design and Development. Combinatorial Chemistry & High Throughput Screening, 13(5), 442-453.