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 2011-2012108. Bras, N. F., Cruz, L., Fernandes, P. A., De Freitas, V., & Ramos, M. J. (2011). Conformational Study of Two Diasteroisomers of Vinylcatechin Dimers in a Methanol Solution. International Journal of Quantum Chemistry, 111(7-8), 1498-1510. doi:10.1002/qua.22631
109. Bras, N. F., Perez, M. A. S., Fernandes, P. A., Silva, P. J., & Ramos, M. J. (2011). Accuracy of Density Functionals in the Prediction of Electronic Proton Affinities of Amino Acid Side Chains. Journal of Chemical Theory and Computation, 7(12), 3898-3908. doi:10.1021/ct200309v
110. Carvalho, A. T. P., Fernandes, P. A., & Ramos, M. J. (2011). The Catalytic Mechanism of RNA Polymerase II. Journal of Chemical Theory and Computation, 7(4), 1177-1188. doi:10.1021/ct100579w
111. Cerqueira, N., Fernandes, P. A., & Ramos, M. J. (2011). Computational Mechanistic Studies Addressed to the Transimination Reaction Present in All Pyridoxal 5 '-Phosphate-Requiring Enzymes. Journal of Chemical Theory and Computation, 7(5), 1356-1368. doi:10.1021/ct1002219
112. Cerqueira, N., Ribeiro, J., Fernandes, P. A., & Ramos, M. J. (2011). vsLab-An Implementation for Virtual High-Throughput Screening Using AutoDock and VMD. International Journal of Quantum Chemistry, 111(6), 1208-1212. doi:10.1002/qua.22738
113. Moorthy, N., Ramos, M. J., & Fernandes, P. A. (2011). Analysis of the alpha-Glucosidase Inhibitory Activity of Chromenone Derivatives Based on their Molecular Features: A Computational Study. Medicinal Chemistry, 7(6), 526-533.
114. Moorthy, N., Ramos, M. J., & Fernandes, P. A. (2011). Structural analysis of alpha-glucosidase inhibitors by validated QSAR models using topological and hydrophobicity based descriptors. Chemometrics and Intelligent Laboratory Systems, 109(2), 101-112. doi:10.1016/j.chemolab.2011.02.010
115. Moorthy, N., Ramos, M. J., & Fernandes, P. A. (2011). Topological, hydrophobicity, and other descriptors on alpha-glucosidase inhibition: a QSAR study on xanthone derivatives. Journal of Enzyme Inhibition and Medicinal Chemistry, 26(6), 755-766. doi:10.3109/14756366.2011.549089
116. Moorthy, N., Ramos, M. J., & Fernandes, P. A. (2011). hERG binding feature analysis of structurally diverse compounds by QSAR and fragmental analysis. Rsc Advances, 1(6), 1126-1136. doi:10.1039/c1ra00131k
117. Moorthy, N., Ramos, M. J., & Fernandes, P. A. (2011). Prediction of the relationship between the structural features of andrographolide derivatives and alpha-glucosidase inhibitory activity: A quantitative structure-activity relationship (QSAR) Study. Journal of Enzyme Inhibition and Medicinal Chemistry, 26(1), 78-87. doi:10.3109/14756361003724760
118. Moorthy, N., Ramos, M. J., & Fernandes, P. A. (2011). QSAR Analysis of Isosteviol Derivatives as alpha-Glucosidase Inhibitors with Element Count and Other Descriptors. Letters in Drug Design & Discovery, 8(1), 14-25.
119. Moorthy, N., Sousa, S. F., Ramos, M. J., & Fernandes, P. A. (2011). Structural feature study of benzofuran derivatives as farnesyltransferase inhibitors. Journal of Enzyme Inhibition and Medicinal Chemistry, 26(6), 777-791. doi:10.3109/14756366.2011.552885
120. Moorthy, N., Sousa, S. F., Ramos, M. J., & Fernandes, P. A. (2011). In Silico-Based Structural Analysis of Arylthiophene Derivatives for FTase Inhibitory Activity, hERG, and Other Toxic Effects. Journal of Biomolecular Screening, 16(9), 1037-1046. doi:10.1177/1087057111414899
121. Neves, A. R., Fernandes, P. A., & Ramos, M. J. (2011). The Accuracy of Density Functional Theory in the Description of Cation-pi and pi-Hydrogen Bond Interactions. Journal of Chemical Theory and Computation, 7(7), 2059-2067. doi:10.1021/ct2001667
122. Oliveira, E. F., Cerqueira, N., Fernandes, P. A., & Ramos, M. J. (2011). Mechanism of Formation of the Internal Aldimine in Pyridoxal 5 '-Phosphate-Dependent Enzymes. Journal of the American Chemical Society, 133(39), 15496-15505. doi:10.1021/ja204229m
123. Oliveira, J., Petrov, V., Parola, A. J., Pina, F., Azevedo, J., Teixeira, N., . . . de Freitas, V. (2011). Chemical Behavior of Methylpyranomalvidin-3-O-glucoside in Aqueous Solution Studied by NMR and UV-Visible Spectroscopy. Journal of Physical Chemistry B, 115(6), 1538-1545. doi:10.1021/jp110593c
124. Passos, O., Fernandes, P. A., & Ramos, M. J. (2011). QM/MM Study of the Catalytic Mechanism of GalNAc Removal from GM2 Ganglioside Catalyzed by Human beta-HexosaminidaseA. Journal of Physical Chemistry B, 115(49), 14751-14759. doi:10.1021/jp205826n
125. Passos, O., Fernandes, P. A., & Ramos, M. J. (2011). Theoretical insights into the catalytic mechanism of beta-hexosaminidase. Theoretical Chemistry Accounts, 129(1), 119-129. doi:10.1007/s00214-011-0904-1
126. Perez, M. A. S., Sousa, S. F., Oliveira, E. F. T., Fernandes, P. A., & Ramos, M. J. (2011). Detection of Farnesyltransferase Interface Hot Spots through Computational Alanine Scanning Mutagenesis. Journal of Physical Chemistry B, 115(51), 15339-15354. doi:10.1021/jp205481y
127. Sousa, S. F., Tamames, B., Fernandes, P. A., & Ramos, M. J. (2011). Detailed Atomistic Analysis of the HIV-1 Protease Interface. Journal of Physical Chemistry B, 115(21), 7045-7057. doi:10.1021/jp200075s
128. Bras, N. F., Ramos, M. J., & Fernandes, P. A. (2012). The catalytic mechanism of mouse renin studied with QM/MM calculations. Physical Chemistry Chemical Physics, 14(36), 12605-12613. doi:10.1039/c2cp41422h
129. De Rienzo, F., Barbosa, A. J. M., Perez, M. A. S., Fernandes, P. A., Ramos, M. J., & Menziani, M. C. (2012). The extracellular subunit interface of the 5-HT3 receptors: a computational alanine scanning mutagenesis study. Journal of Biomolecular Structure & Dynamics, 30(3), 280-298. doi:10.1080/07391102.2012.680029
130. Gesto, D. S., Cerqueira, N., Fernandes, P. A., & Ramos, M. J. (2012). Gemcitabine: A Critical Nucleoside for Cancer Therapy. Current Medicinal Chemistry, 19(7), 1076-1087.
131. Moorthy, N., Bras, N. F., Ramos, M. J., & Fernandes, P. A. (2012). Virtual screening and QSAR study of some pyrrolidine derivatives as alpha-mannosidase inhibitors for binding feature analysis. Bioorganic & Medicinal Chemistry, 20(24), 6945-6959. doi:10.1016/j.bmc.2012.10.011
132. Moorthy, N., Cerqueira, N., Ramos, M. J., & Fernandes, P. A. (2012). QSAR and pharmacophore analysis of thiosemicarbazone derivatives as ribonucleotide reductase inhibitors. Medicinal Chemistry Research, 21(6), 739-746. doi:10.1007/s00044-011-9580-x
133. Moorthy, N., Cerqueira, N. S., Ramos, M. J., & Fernandes, P. A. (2012). QSAR analysis of 2-benzoxazolyl hydrazone derivatives for anticancer activity and its possible target prediction. Medicinal Chemistry Research, 21(2), 133-144. doi:10.1007/s00044-010-9510-3
134. Moorthy, N., Ramos, M. J., & Fernandes, P. A. (2012). Structural analysis of structurally diverse alpha-glucosidase inhibitors for active site feature analysis. Journal of Enzyme Inhibition and Medicinal Chemistry, 27(5), 649-657. doi:10.3109/14756366.2011.605359
135. Moorthy, N., Ramos, M. J., & Fernandes, P. A. (2012). Analysis of van der Waals surface area properties for human ether-a-go-go-related gene blocking activity: computational study on structurally diverse compounds. Sar and Qsar in Environmental Research, 23(5-6), 521-536. doi:10.1080/1062936x.2012.666264
136. Moorthy, N., Ramos, M. J., & Fernandes, P. A. (2012). Studies on alpha-Glucosidase Inhibitors Development: Magic Molecules for the Treatment of Carbohydrate Mediated Diseases. Mini-Reviews in Medicinal Chemistry, 12(8), 713-720.
137. Moorthy, N., Ramos, M. J., & Fernandes, P. A. (2012). Comparative Structural Analysis of a-Glucosidase Inhibitors on Difference Species: A Computational Study. Archiv Der Pharmazie, 345(4), 265-274. doi:10.1002/ardp.201100047
138. Moorthy, N., Sousa, S. F., Ramos, M. J., & Fernandes, P. A. (2012). In silico Based Structural Analysis of Some Piperidine Analogs as Farnesyltransferase Inhibitors. Medicinal Chemistry, 8(5), 853-864.
139. Ribeiro, A. J. M., Ramos, M. J., & Fernandes, P. A. (2012). The Catalytic Mechanism of HIV-1 Integrase for DNA 3 '-End Processing Established by QM/MM Calculations. Journal of the American Chemical Society, 134(32), 13436-13447. doi:10.1021/ja304601k
140. Ribeiro, J. V., Cerqueira, N., Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2012). CompASM: an Amber-VMD alanine scanning mutagenesis plug-in. Theoretical Chemistry Accounts, 131(10). doi:10.1007/s00214-012-1271-2
141. Silva, P. J., Perez, M. A. S., Bras, N. F., Fernandes, P. A., & Ramos, M. J. (2012). Improving the study of proton transfers between amino acid side chains in solution: choosing appropriate DFT functionals and avoiding hidden pitfalls. Theoretical Chemistry Accounts, 131(3). doi:10.1007/s00214-012-1179-x
142. Sousa, S. F., Fernandes, P. A., & Ramos, M. J. (2012). Computational enzymatic catalysis - clarifying enzymatic mechanisms with the help of computers. Physical Chemistry Chemical Physics, 14(36), 12431-12441. doi:10.1039/c2cp41180f
143. Zhang, W., Dourado, D., Fernandes, P. A., Ramos, M. J., & Mannervik, B. (2012). Multidimensional epistasis and fitness landscapes in enzyme evolution. Biochemical Journal, 445, 39-46. doi:10.1042/bj20120136