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 2013-2014163. Ramos, M. J. (2013). Molecular dynamics analysis of a series of 22 potential farnesyltransferase substrates containing a CaaX-motif. Journal of Molecular Modeling, 19(2), 673-688. doi:10.1007/s00894-012-1590-1
164. Sousa, S. F., Pinto, G. R. P., Ribeiro, A. J. M., Coimbra, J. T. S., Fernandes, P. A., & Ramos, M. J. (2013). Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes. Journal of Computational Chemistry, 34(24), 2079-2090. doi:10.1002/jcc.23349
165. Sousa, S. F., Ribeiro, A. J. M., Coimbra, J. T. S., Neves, R. P. P., Martins, S. A., Moorthy, N., . . . Ramos, M. J. (2013). Protein-Ligand Docking in the New Millennium - A Retrospective of 10 Years in the Field. Current Medicinal Chemistry, 20(18), 2296-2314. doi:10.2174/0929867311320180002
166. Aranda, J., Cerqueira, N., Fernandes, P. A., Roca, M., Tunon, I., & Ramos, M. J. (2014). The Catalytic Mechanism of Carboxylesterases: A Computational Study. Biochemistry, 53(36), 5820-5829. doi:10.1021/bi500934j
167. Araujo, A. R., Ribeiro, A. J. M., Fernandes, P. A., & Ramos, M. J. (2014). Catalytic Mechanism of Retroviral Integrase for the Strand Transfer Reaction Explored by QM/MM Calculations. Journal of Chemical Theory and Computation, 10(12), 5458-5466. doi:10.1021/ct500570g
168. Bras, N. F., Cerqueira, N., Ramos, M. J., & Fernandes, P. A. (2014). Glycosidase inhibitors: a patent review (2008-2013). Expert Opinion on Therapeutic Patents, 24(8), 857-874. doi:10.1517/13543776.2014.916280
169. Bras, N. F., Fernandes, P. A., & Ramos, M. J. (2014). QM/MM Study and MD Simulations on the Hypertension Regulator Angiotensin-Converting Enzyme. Acs Catalysis, 4(8), 2587-2597. doi:10.1021/cs500093h
170. Bras, N. F., Fernandes, P. A., & Ramos, M. J. (2014). Discovery of New Sites for Drug Binding to the Hypertension-Related Renin-Angiotensinogen Complex. Chemical Biology & Drug Design, 83(4), 427-439. doi:10.1111/cbdd.12258
171. Bras, N. F., Fernandes, P. A., & Ramos, M. J. (2014). Molecular dynamics studies on both bound and unbound renin protease. Journal of Biomolecular Structure & Dynamics, 32(3), 351-363. doi:10.1080/07391102.2013.768553
172. Bras, N. F., Ribeiro, A. J. M., Oliveira, M., Paixao, N. M., Tamames, J. A., Fernandes, P. A., & Ramos, M. J. (2014). Analyses of cobalt-ligand and potassium-ligand bond lengths in metalloproteins: trends and patterns. Journal of Molecular Modeling, 20(6). doi:10.1007/s00894-014-2271-z
173. Calixto, A. R., Bras, N. F., Fernandes, P. A., & Ramos, M. J. (2014). Reaction Mechanism of Human Renin Studied by Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations. Acs Catalysis, 4(11), 3869-3876. doi:10.1021/cs500497f
174. Coimbra, J. T. S., Moniz, T., Bras, N. F., Iyanova, G., Fernandes, P. A., Ramos, M. J., & Rangel, M. (2014). Relevant Interactions of Antimicrobial Iron Chelators and Membrane Models Revealed by Nuclear Magnetic Resonance and Molecular Dynamics Simulations. Journal of Physical Chemistry B, 118(50), 14590-14601. doi:10.1021/jp509491p
175. Coimbra, J. T. S., Neves, R. P. P., Passos, O., Jarukanont, D., Fernandes, P. A., Patel, S., . . . Ramos, M. J. (2014). Influence of the environment on protein bond energies. Chemical Physics Letters, 615, 75-82. doi:10.1016/j.cplett.2014.09.066
176. Coimbra, J. T. S., Sousa, S. F., Fernandes, P. A., Rangel, M., & Ramos, M. J. (2014). Biomembrane simulations of 12 lipid types using the general amber force field in a tensionless ensemble. Journal of Biomolecular Structure & Dynamics, 32(1), 88-103. doi:10.1080/07391102.2012.750250
177. Dourado, D., Fernandes, P. A., Mannervik, B., & Ramos, M. J. (2014). Isomerization of Delta(5)-Androstene-3,17-dione into Delta(4)-Androstene-3, 17-dione Catalyzed by Human Glutathione Transferase A3-3: A Computational Study Identifies a Dual Role for Glutathione. Journal of Physical Chemistry A, 118(31), 5790-5800. doi:10.1021/jp410810q
178. Gesto, D. S., Cerqueira, N., Ramos, M. J., & Fernandes, P. A. (2014). Discovery of new druggable sites in the anti-cholesterol target HMG-CoA reductase by computational alanine scanning mutagenesis. Journal of Molecular Modeling, 20(4). doi:10.1007/s00894-014-2178-8
179. Hong, M. K., Ribeiro, A. J. M., Kim, J. K., Ngo, H. P. T., Kim, J., Lee, C. H., . . . Kang, L. W. (2014). Divalent metal ion-based catalytic mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli. Acta Crystallographica Section D-Biological Crystallography, 70, 1297-1310. doi:10.1107/s1399004714002570
180. Jarukanont, D., Coimbra, J. T. S., Bauerhenne, B., Fernandes, P. A., Patel, S., Ramos, M. J., & Garcia, M. E. (2014). Biomolecular structure manipulation using tailored electromagnetic radiation: a proof of concept on a simplified model of the active site of bacterial DNA topoisomerase. Physical Chemistry Chemical Physics, 16(39), 21768-21777. doi:10.1039/c4cp02289k
181. Martins, S. A., Sousa, S. F., Ramos, M. J., & Fernandes, P. A. (2014). Prediction of Solvation Free Energies with Thermodynamic Integration Using the General Amber Force Field. Journal of Chemical Theory and Computation, 10(8), 3570-3577. doi:10.1021/ct500346y
182. Moorthy, N., Bras, N. F., Ramos, M. J., & Fernandes, P. A. (2014). Binding mode prediction and identification of new lead compounds from natural products as renin and angiotensin converting enzyme inhibitors. Rsc Advances, 4(38), 19550-19568. doi:10.1039/c4ra00856a
183. Moorthy, N., Martins, S. A., Sousa, S. F., Ramos, M. J., & Fernandes, P. A. (2014). Classification study of solvation free energies of organic molecules using machine learning techniques. Rsc Advances, 4(106), 61624-61630. doi:10.1039/c4ra07961b
184. Moorthy, N., Pratheepa, V., Ramos, M. J., Vasconcelos, V., & Fernandes, P. A. (2014). Fused Aryl-Phenazines: Scaffold for the Development of Bioactive Molecules. Current Drug Targets, 15(7), 681-688. doi:10.2174/1389450115666140205152007
185. Moorthy, N., Ramos, M. J., & Fernandes, P. A. (2014). Predictive QSAR models development and validation for human ether-a-go-go related gene (hERG) blockers using newer tools. Journal of Enzyme Inhibition and Medicinal Chemistry, 29(3), 317-324. doi:10.3109/14756366.2013.779264
186. Moreira, I. S., Ramos, R. M., Martins, J. M., Fernandes, P. A., & Ramos, M. J. (2014). Are hot-spots occluded from water? Journal of Biomolecular Structure & Dynamics, 32(2), 186-197. doi:10.1080/07391102.2012.758598
187. Neves, R. P. P., Fernandes, P. A., Varandas, A. J. C., & Ramos, M. J. (2014). Benchmarking of Density Functionals for the Accurate Description of Thiol-Disulfide Exchange. Journal of Chemical Theory and Computation, 10(11), 4842-4856. doi:10.1021/ct500840f
188. Ngo, H. P. T., Cerqueira, N., Kim, J. K., Hong, M. K., Fernandes, P. A., Ramos, M. J., & Kang, L. W. (2014). PLP undergoes conformational changes during the course of an enzymatic reaction. Acta Crystallographica Section D-Biological Crystallography, 70, 596-606. doi:10.1107/s1399004713031283
189. Ribeiro, J. V., Cerqueira, N., Fernandes, P. A., & Ramos, M. J. (2014). chem-path-tracker: An Automated Tool to Analyze Chemical Motifs in Molecular Structures. Chemical Biology & Drug Design, 84(1), 44-53. doi:10.1111/cbdd.12349
190. Silva, A. M. N., Sousa, P. R. H., Coimbra, J. T. S., Bras, N. F., Vitorino, R., Fernandes, P. A., . . . Domingues, P. (2014). The glycation site specificity of human serum transferrin is a determinant for transferrin's functional impairment under elevated glycaemic conditions. Biochemical Journal, 461, 33-42. doi:10.1042/bj20140133
191. Sousa, S. F., Cerqueira, N., Bras, N. F., Fernandes, P. A., & Ramos, M. J. (2014). Enzymatic "Tricks": Carboxylate Shift and Sulfur Shift. International Journal of Quantum Chemistry, 114(19), 1253-1256. doi:10.1002/qua.24689