Selected Publications
Below is a selection of my publications, listed by date and updated on the 13/May/2014.
2019-2020| 2017-2018| 2015-2016| 2013-2014| 2011-2012| 2009-2010| 2007-2008| 2005-2006| 2003-2004| 2000-2002|Publications 2009-2010
Dourado, DFAR; Fernandes, PA; Ramos, MJ, Glutathione Transferase Classes Alpha, Pi, and Mu: GSH Activation Mechanism, JOURNAL OF PHYSICAL CHEMISTRY B, 114 (40), 12972-12980 2010
Bras, NF; Goncalves, R; Mateus, N; Ramos, MJ; Dangles, O; De Freitas, V, Inhibition of Pancreatic Elastase by Polyphenolic Compounds, JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 58 (19), 10668-10676 2010
Perez, MAS; Fernandes, PA; Ramos, MJ, Understanding the Mechanism for Ribonucleotide Reductase Inactivation by 2 '-Deoxy-2 '-methylenecytidine-5 '-diphosphate, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6 (9), 2770-2781 2010
Ramos, MJ, Computational enzymatic catalysis, FEBS JOURNAL, 277, 25 2010
Alberto, ME; Marino, T; Ramos, MJ; Russo, N, Atomistic details of the Catalytic Mechanism of Fe(III)-Zn(II) Purple Acid Phosphatase, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6 (8), 2424-2433 2010
Ribeiro, AJM; Ramos, MJ; Fernandes, PA, Benchmarking of DFT Functionals for the Hydrolysis of Phosphodiester Bonds, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6 (8), 2281-2292 2010
Perez, MAS; Cerqueira, NMFSA; Fernandes, PA; Ramos, MJ, Ribonucleotide Reductase: A Mechanistic Portrait of Substrate Analogues Inhibitors, CURRENT MEDICINAL CHEMISTRY, 17 (26), 2854-2872 2010
Marques, AT; Fernandes, PA; Ramos, MJ, Structural Analysis of ABAD Point Mutations Causing 2-Methyl-3-hydroxylbutyryl-coA Deficiency, INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 110 (1), 148-160 2010
Moreira, IS; Fernandes, PA; Ramos, MJ, Protein-Protein Docking Dealing With the Unknown, JOURNAL OF COMPUTATIONAL CHEMISTRY, 31 (2), 317-342 2010
Dourado, DFAR; Fernandes, PA; Mannervik, B; Ramos, MJ, Glutathione Transferase A1-1: Catalytic Importance of Arginine 15, JOURNAL OF PHYSICAL CHEMISTRY B, 114 (4), 1690-1697 2010
Perez, MAS; Fernandes, PA; Ramos, MJ, Substrate Recognition in HIV-1 Protease: A Computational Study, JOURNAL OF PHYSICAL CHEMISTRY B, 114 (7), 2525-2532 2010
Bras, NF; Fernandes, PA; Ramos, MJ, QM/MM Studies on the beta-Galactosidase Catalytic Mechanism: Hydrolysis and Transglycosylation Reactions, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6 (2), 421-433 2010
Cruz, L; Bras, NF; Teixeira, N; Ramos, MJ; Freitas, V, Vinylcatechin Dimers Are Much Better Copigments for Anthocyanins than Catechin Dimer Procyanidin B3, JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 58 (5), 3159-3166 2010
Bras, NF; Ramos, MJ; Fernandes, PA, DFT studies on the beta-glycosidase catalytic mechanism: The deglycosylation step, JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 946 (1-3), 125-133 2010
Sousa, SF; Cerqueira, NMFSA; Fernandes, PA; Ramos, MJ, Virtual Screening in Drug Design and Development, COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING, 13 (5), 442-453 2010
Bras, NF; Goncalves, R; Fernandes, PA; Ramos, MJ; Freitas, V, Understanding the Binding of Procyanidins to Pancreatic Elastase by Experimental and Computational Methods, BIOCHEMISTRY, 49 (25), 5097-5108 2010
Silva, PJ; Schulz, C; Jahn, D; Jahn, M; Ramos, MJ, A Tale of Two Acids: When Arginine Is a More Appropriate Acid than H3O+, JOURNAL OF PHYSICAL CHEMISTRY B, 114 (27), 8994-9001 2010
Barbosa, AJM; De Rienzo, F; Ramos, MJ; Menziani, MC, Computational analysis of ligand recognition sites of homo- and heteropentameric 5-HT3 receptors, EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY Volume: 45 Issue: 11 Pages: 4746-4760 Published: 2010
Sousa, SF; Fernandes, PA; Ramos, MJ, The Search for the Mechanism of the Reaction Catalyzed by Farnesyltransferase, CHEMISTRY-A EUROPEAN JOURNAL,15 (17) 4243-4247 2009
Sousa, SF; Fernandes, PA; Ramos, MJ, Molecular dynamics simulations on the critical states of the farnesyltransferase enzyme, BIOORGANIC & MEDICINAL CHEMISTRY, 17(9) 3369-3378 2009
Carvalho, ATP; Fernandes, PA; Swart, M; van Stralen, JNP; Bickelhaupt FM; Ramos MJ
Role of the Variable Active Site Residues in the Function of Thioredoxin Family Oxidoreductases
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30 (5) 710-724 2009
Cerqueira, NMFSA; Fernandes PA; Ramos, MJ, MADAMM: a Multi stAged Docking with an Automated Molecular Modelling Protocol, PROTEINS-STRUCTURE, FUNCTION AND BIOINFORMATICS, 74 (1):192-206 2009
Moura-Tamames, SA; Ramos, MJ; Fernandes, PA, 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 2009
Marques, AT; Fernandes, PA; Ramos, MJ, ABAD: A Potential Therapeutic Target for A beta-Induced Mitochondrial Dysfunction in Alzheimer's Disease, MINI-REVIEWS IN MEDICINAL CHEMISTRY, 9 (8):1002-1008 2009
Moura-Tamames, S; Ramos, MJ; Fernades, PA, 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 2009
Tamames, B; Fernandes, PA; Ramos, MJ, HIV-1 Protease: a computational mutagenesis analysis of the monomers interface, FEBS JOURNAL, 276: 167-167 2009
Silva, PJ; Ramos, MJ, Computational Studies on the Reactivity of Substituted 1,2-Dihydro-1,2-azaborines, JOURNAL OF ORGANIC CHEMISTRY, 74 (16): 6120-6129 2009
Dourado, DFAR; Fernandes, PA; Ramos, MJ, Glutathione transferase A1-1: catalytic role of water, THEORETICAL CHEMISTRY ACCOUNTS, 124 (1-2): 71-83 2009
Sousa, SF; Lopes, AB; Fernandes, PA; Ramos, MJ, The Zinc proteome: a tale of stability and functionality, DALTON TRANSACTIONS (38): 7946-7956 2009
Sousa, SF; Carvalho, ES; Ferreira, DM; Tavares, IS; Fernandes, PA; Ramos, MJ; Gomes, JANF 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 2009
Cruz, L; Bras, NF; Teixeira, N; Fernandes, A; Mateus, N; Ramos, MJ; Rodriguez-Borges, J; Freitas, V, Synthesis and Structural Characterization of Two Diasteroisomers of Vinylcatechin Dimers, JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 57 (21): 10341-10348 2009
Pande, V; Sousa, SF; Ramos, MJ, Direct Covalent Modification as a Strategy to Inhibit Nuclear Factor-Kappa B, CURRENT MEDICINAL CHEMISTRY, 16 (32): 4261-4273 2009
Sousa, SF; Fernandes, PA; Ramos, MJ, 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 2009
Sousa, SF; Cerqueira, NMFSA; Perez, MAS; Moreira, IS; Ribeiro, AJMR; Neves, ARAP; Ramos, MJ; Fernandes, PA, Recent Advances on Computational Proteomics, World Academy of Science, Engineering and Technology, Vol. 56, pp. 376-386, 2009
Cerqueira, MNFSA; Sousa, SF; Fernandes, PA; Ramos MJ, Virtual Screening of Compound Libraries, in ‘Ligand Macromolecule Interactions’, ed. Cecília Roque, Humana Press, 2009
Brás, NF; Fernandes, PA; Ramos, MJ, Docking and Molecular Dynamics Studies on the Regioselectivity in the Enzymatic Synthesis of Carbohydrates, THEORETICAL CHEMISTRY ACCOUNTS, 122 (5-6) 283-296 2009
Cerqueira, NMFSA; Fernandes PA; Ramos, MJ, MADAMM: a Multi stAged Docking with an Automated Molecular Modelling Protocol, PROTEINS-STRUCTURE, FUNCTION AND BIOINFORMATICS, 74 (1):192-206 2009