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 2015-2017192. Cerqueira, N., Coelho, C., Bras, N. F., Fernandes, P. A., Garattini, E., Terao, M., . . . Ramos, M. J. (2015). Insights into the structural determinants of substrate specificity and activity in mouse aldehyde oxidases. Journal of Biological Inorganic Chemistry, 20(2), 209-217. doi:10.1007/s00775-014-1198-2
193. Cerqueira, N., Gesto, D., Oliveira, E. F., Santos-Martins, D., Bras, N. F., Sousa, S. F., . . . Ramos, M. J. (2015). Receptor-based virtual screening protocol for drug discovery. Archives of Biochemistry and Biophysics, 582, 56-67. doi:10.1016/j.abb.2015.05.011
194. Cerqueira, N., Gonzalez, P. J., Fernandes, P. A., Moura, J. J. G., & Ramos, M. J. (2015). Periplasmic Nitrate Reductase and Formate Dehydrogenase: Similar Molecular Architectures with Very Different Enzymatic Activities. Accounts of Chemical Research, 48(11), 2875-2884. doi:10.1021/acs.accounts.5b00333
195. Moorthy, N., Cerqueira, N., Ramos, M. J., & Fernandes, P. A. (2015). Ligand based analysis on HMG-CoA reductase inhibitors. Chemometrics and Intelligent Laboratory Systems, 140, 102-116. doi:10.1016/j.chemolab.2014.11.009
196. Moreira, I. S., Martins, J. M., Coimbra, J. T. S., Ramos, M. J., & Fernandes, P. A. (2015). A new scoring function for protein-protein docking that identifies native structures with unprecedented accuracy. Physical Chemistry Chemical Physics, 17(4), 2378-2387. doi:10.1039/c4cp04688a
197. Oliveira, B. L., Morais, M., Mendes, F., Moreira, I. S., Cordeiro, C., Fernandes, P. A., . . . Correia, J. D. G. (2015). Re(I) and Tc(I) Complexes for Targeting Nitric Oxide Synthase: Influence of the Chelator in the Affinity for the Enzyme. Chemical Biology & Drug Design, 86(5), 1072-1086. doi:10.1111/cbdd.12575
198. Pinto, G. P., Bras, N. F., Perez, M. A. S., Fernandes, P. A., Russo, N., Ramos, M. J., & Toscano, M. (2015). Establishing the Catalytic Mechanism of Human Pancreatic alpha-Amylase with QM/MM Methods. Journal of Chemical Theory and Computation, 11(6), 2508-2516. doi:10.1021/acs.jctc.5b00222
199. Pinto, G. P., Ribeiro, A. J. M., Ramos, M. J., Fernandes, P. A., Toscano, M., & Russo, N. (2015). New insights in the catalytic mechanism of tyrosine ammonia-lyase given by QM/MM and QM cluster models. Archives of Biochemistry and Biophysics, 582, 107-115. doi:10.1016/j.abb.2015.03.002
200. Ribeiro, A. J. M., Santos-Martins, D., Russo, N., Rarnos, M. J., & Fernandes, P. A. (2015). Enzymatic Flexibility and Reaction Rate: A QM/MM Study of HIV-1 Protease. Acs Catalysis, 5(9), 5617-5626. doi:10.1021/acscatal.5b00759
201. Ribeiro, A. J. M., Yang, L. F., Ramos, M. J., Fernandes, P. A., Liang, Z. X., & Hirao, H. (2015). Insight into Enzymatic Nitrile Reduction: QM/MM Study of the Catalytic Mechanism of QueF Nitrile Reductase. Acs Catalysis, 5(6), 3740-3751. doi:10.1021/acscatal.5b00528
202. Shi, Y. X., Liang, R. Z., Martin, K. A., Weston, N., Gonzalez-Calera, S., Ganguly, R., . . . Garcia, F. (2015). Synthesis and Hydrolytic Studies on the Air-Stable (4-CN-PhO)(E)P(mu-(NBu)-Bu-t) (2) (E = O, S, and Se) Cyclodiphosphazanes. Inorganic Chemistry, 54(13), 6423-6432. doi:10.1021/acs.inorgchem.5b00735
203. Sousa, S. F., Coimbra, J. T. S., Fernandes, P. A., Marino, T., Ramos, M. J., & Russo, N. (2015). Molecular Dynamics Analysis of FAAH Complexed with Anandamide. In M. A. C. Nascimento, J. Maruani, E. J. Brandas, & G. DelgadoBarrio (Eds.), Frontiers in Quantum Methods and Applications in Chemistry and Physics (Vol. 29, pp. 114-130).
204. Sousa, S. F., Ramos, M. J., Lim, C., & Fernandes, P. A. (2015). Relationship between Enzyme/Substrate Properties and Enzyme Efficiency in Hydrolases. Acs Catalysis, 5(10), 5877-5887. doi:10.1021/acscatal.5b00923
205. Bras, N. F., Ferreira, P., Calixto, A. R., Jaspars, M., Houssen, W., Naismith, J. H., . . . Ramos, M. J. (2016). The Catalytic Mechanism of the Marine-Derived Macrocyclase PatGmac. Chemistry-a European Journal, 22(37), 13089-13097. doi:10.1002/chem.201601670
206. Cerqueira, N., Oliveira, E. F., Gesto, D. S., Santos-Martins, D., Moreira, C., Moorthy, H. N., . . . Fernandes, P. A. (2016). Cholesterol Biosynthesis: A Mechanistic Overview. Biochemistry, 55(39), 5483-5506. doi:10.1021/acs.biochem.6b00342
207. Llinas, P., Chenon, M., Nguyen, T. Q., Moreira, C., de Regibus, A., Coquard, A., . . . Menetrey, J. (2016). Structure of a truncated form of leucine zipper II of JIP3 reveals an unexpected antiparallel coiled-coil arrangement. Acta Crystallographica Section F-Structural Biology Communications, 72, 198-206. doi:10.1107/s2053230x16001576
208. Moniz, T., Coimbra, J. T. S., Bras, N. F., Cunha-Silva, L., Ramos, M. J., Fernandes, P. A., . . . Rangel, M. (2016). Synthesis and structural characterization, by spectroscopic and computational methods, of two fluorescent 3-hydroxy-4-pyridinone chelators bearing sulphorhodamine B and naphthalene. Rsc Advances, 6(5), 4200-4211. doi:10.1039/c5ra23217a
209. Moorthy, N., Sousa, S. F., Ramos, M. J., & Fernandes, P. A. (2016). Molecular dynamic simulations and structure-based pharmacophore development for farnesyltransferase inhibitors discovery. Journal of Enzyme Inhibition and Medicinal Chemistry, 31(6), 1428-1442. doi:10.3109/14756366.2016.1144593
210. Moorthy, N., Sousa, S. F., Ramos, M. J., & Fernandes, P. A. (2016). Binding mode of conformations and structure-based pharmacophore development for farnesyltransferase inhibitors. Medicinal Chemistry Research, 25(7), 1340-1357. doi:10.1007/s00044-016-1578-y
211. Moreira, C., Ramos, M. J., & Fernandes, P. A. (2016). Glutamine Synthetase Drugability beyond Its Active Site: Exploring Oligomerization Interfaces and Pockets. Molecules, 21(8). doi:10.3390/molecules21081028
212. Moreira, C., Ramos, M. J., & Fernandes, P. A. (2016). Reaction Mechanism of Mycobacterium Tuberculosis Glutamine Synthetase Using Quantum Mechanics/Molecular Mechanics Calculations. Chemistry-a European Journal, 22(27), 9218-9225. doi:10.1002/chem.201600305
213. Neves, R. P. P., Fernandes, P. A., & Ramos, M. J. (2016). Unveiling the Catalytic Mechanism of NADP(+)-Dependent Isocitrate Dehydrogenase with QM/MM Calculations. Acs Catalysis, 6(1), 357-368. doi:10.1021/acscatal.5b01928
214. Oliveira, E. F., Cerqueira, N., Ramos, M. J., & Fernandes, P. A. (2016). QM/MM study of the mechanism of reduction of 3-hydroxy-3-methylglutaryl coenzyme A catalyzed by human HMG-CoA reductase. Catalysis Science & Technology, 6(19), 7172-7185. doi:10.1039/c6cy00356g
215. Oliveira, E. F., Santos-Martins, D., Ribeiro, A. M., Bras, N. F., Cerqueira, N. S., Sousa, S. F., . . . Fernandes, P. A. (2016). HMG-CoA Reductase inhibitors: an updated review of patents of novel compounds and formulations (2011-2015). Expert Opinion on Therapeutic Patents, 26(11), 1257-1272. doi:10.1080/13543776.2016.1216977
216. Santos-Martins, D., Fernandes, P. A., & Ramos, M. J. (2016). Calculation of distribution coefficients in the SAMPL5 challenge from atomic solvation parameters and surface areas. Journal of Computer-Aided Molecular Design, 30(11), 1079-1086. doi:10.1007/s10822-016-9951-y
217. Sousa, R. P., Fernandes, P. A., Ramos, M. J., & Bras, N. F. (2016). Insights into the reaction mechanism of 3-O-sulfotransferase through QM/MM calculations. Physical Chemistry Chemical Physics, 18(16), 11488-11496. doi:10.1039/c5cp06224a
218. Sousa, S. F., Sousa, J. F. M., Barbosa, A. C. C., Ferreira, C. E., Neves, R. P. P., Ribeiro, A. J. M., . . . Ramos, M. J. (2016). Improving the Biodesulfurization of Crude Oil and Derivatives: A QM/MM Investigation of the Catalytic Mechanism of NADH-FMN Oxidoreductase (DszD). Journal of Physical Chemistry A, 120(27), 5300-5306. doi:10.1021/acs.jpca.6b01536
219. Barra, P. A., Ribeiro, A. J. M., Ramos, M. J., Jimenez, V. A., Alderete, J. B., & Fernandes, P. A. (2017). Binding free energy calculations on E-selectin complexes with sLe(x) oligosaccharide analogs. Chemical Biology & Drug Design, 89(1), 114-123. doi:10.1111/cbdd.12837
220. Calixto, A. R., Ramos, M. J., & Fernandes, P. A. (2017). Influence of Frozen Residues on the Exploration of the PES of Enzyme Reaction Mechanisms. Journal of Chemical Theory and Computation, 13(11), 5486-5495. doi:10.1021/acs.jctc.7b00768
221. Cerqueira, N., Moorthy, H., Fernandes, P. A., & Ramos, M. J. (2017). The mechanism of the Ser-(cis)Ser-Lys catalytic triad of peptide amidases. Physical Chemistry Chemical Physics, 19(19), 12343-12354. doi:10.1039/c7cp00277g
222. Coimbra, J. T. S., Fernandes, P. A., & Ramos, M. J. (2017). Revisiting Partition in Hydrated Bilayer Systems. Journal of Chemical Theory and Computation, 13(5), 2290-2299. doi:10.1021/acs.jctc.6b01258
223. Fernandes, H. S., Teixeira, C. S. S., Fernandes, P. A., Ramos, M. J., & Cerqueira, N. (2017). Amino acid deprivation using enzymes as a targeted therapy for cancer and viral infections. Expert Opinion on Therapeutic Patents, 27(3), 283-297. doi:10.1080/13543776.2017.1254194
224. Ferreira, P., Sousa, S. F., Fernandes, P. A., & Ramos, M. J. (2017). Improving the Catalytic Power of the DszD Enzyme for the Biodesulfurization of Crude Oil and Derivatives. Chemistry-a European Journal, 23(68), 17231-17241. doi:10.1002/chem.201704057
225. Hu, Z., Sim, Y., Kon, O. L., Ng, W. H., Ribeiro, A. J. M., Ramos, M. J., . . . Yeow, E. K. L. (2017). Unique Triphenylphosphonium Derivatives for Enhanced Mitochondrial Uptake and Photodynamic Therapy. Bioconjugate Chemistry, 28(2), 590-599. doi:10.1021/acs.bioconjchem.6b00682
226. Medina, F. E., Neves, R. P. P., Ramos, M. J., & Fernandes, P. A. (2017). A QM/MM study of the reaction mechanism of human beta-ketoacyl reductase. Physical Chemistry Chemical Physics, 19(1), 347-355. doi:10.1039/c6cp07014k
227. Merski, M., Moreira, C., Abreu, R. M. V., Ramos, M. J., Fernandes, P. A., Martins, L. M., . . . Macedo-Ribeiro, S. (2017). Molecular motion regulates the activity of the Mitochondrial Serine Protease HtrA2. Cell Death & Disease, 8. doi:10.1038/cddis.2017.487
228. Moreira, C., Ramos, M. J., & Fernandes, P. A. (2017). Clarifying the Catalytic Mechanism of Human Glutamine Synthetase: A QM/MM Study. Journal of Physical Chemistry B, 121(26), 6313-6320. doi:10.1021/acs.jpcb.7b02543
229. Neves, R. P. P., Fernandes, P. A., & Ramos, M. J. (2017). Mechanistic insights on the reduction of glutathione disulfide by protein disulfide isomerase. Proceedings of the National Academy of Sciences of the United States of America, 114(24), E4724-E4733. doi:10.1073/pnas.1618985114
230. Pereira, A. T., Ribeiro, A. J. M., Fernandes, P. A., & Ramos, M. J. (2017). Benchmarking of density functionals for the kinetics and thermodynamics of the hydrolysis of glycosidic bonds catalyzed by glycosidases. International Journal of Quantum Chemistry, 117(18). doi:10.1002/qua.25409
231. Ribeiro, R. P., Coimbra, J. T. S., Ramos, M. J., & Fernandes, P. A. (2017). Diffusion of the small, very polar, drug piracetam through a lipid bilayer: an MD simulation study. Theoretical Chemistry Accounts, 136(4). doi:10.1007/s00214-017-2073-3
232. Simoes, I. C. M., Costa, I. P. D., Coimbra, J. T. S., Ramos, M. J., & Fernandes, P. A. (2017). New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein-Protein Interfaces. Journal of Chemical Information and Modeling, 57(1), 60-72. doi:10.1021/acs.jcim.6b00378
233. Sousa, C. F., Coimbra, J. T. S., Ferreira, M., Ramos, M. J., Fernandes, P. A., & Gameiro, P. (2017). Exploring the permeation of free and copper-complexed fluoroquinolones across the bacterial membrane. European Biophysics Journal with Biophysics Letters, 46, S269-S269.
234. Sousa, C. F., Coimbra, J. T. S., Gomes, I., Franco, R., Fernandes, P. A., & Gameiro, P. (2017). The binding of free and copper-complexed fluoroquinolones to OmpF porins: an experimental and molecular docking study. Rsc Advances, 7(17), 10009-10019. doi:10.1039/c6ra26466b
235. Sousa, S. F., Ribeiro, A. J. M., Neves, R. P. P., Bras, N. F., Cerqueira, N., Fernandes, P. A., & Ramos, M. J. (2017). Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms. Wiley Interdisciplinary Reviews-Computational Molecular Science, 7(2). doi:10.1002/wcms.1281