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 2018-2020236. HC Ong, Z Hu, JTS Coimbra, MJ Ramos, OL Kon, B Xing, E Yeow, PA Fernandes, F Garcia, Enabling mitochondrial uptake of lipophilic dications using methylated triphenylphosphonium moieties, Inorganic Chemistry, in press, 2019.
237. AR Calixto, MJ Ramos, PA Fernandes, Conformational Diversity Induces Nanosecond-Timescale Chemical Disorder in the HIV-1 Protease Reaction Pathway, Chemical Science, in press, 2019.
238. P Paiva , SF Sousa, PA Fernandes, MJ Ramos, Human Fatty Acid Synthase a computational study of the transfer of the acyl moieties from MAT to the ACP domain, ChemCatChem, in press, 2019
239. MJJ Ramos, P Ferreira, NMFAS Cerqueira, PA Fernandes, C Coelho, MJ Romão, New insights about the monomer and homodimer structures of the human AOX1, Physical Chemistry Chemical Physics, in press, 2019
240. JTS Coimbra, NF Brás, PA Fernandes, M Rangel, MJ Ramos, A computational study on the redox properties and binding affinities of iron complexes of hydroxypyridinones, Journal of Molecular Modeling 25 (6), 172 , 2019
241. SF Sousa, RPP Neves, SO Waheed, PA Fernandes, MJ Ramos , Structural and mechanistic aspects of SS bonds in the thioredoxin-like family of proteins, Biological Chemistry 400 (5), 575-587, 2019
242. KA Wilson, PA Fernandes, MJ Ramos, SD Wetmore, Exploring the Identity of the General Base for a DNA Polymerase Catalyzed Reaction Using QM/MM: The Case Study of Human Translesion Synthesis Polymerase eta, ACS Catalysis 9 (3), 2543-2551, 2019
243. P Gameiro, CF Sousa, JTS Coimbra, PA Fernandes, MJ Ramos, Drug Permeation Across the Bacterial Membrane: Combining Theoretical and Experimental Approaches, Biophysical Journal 116 (3), 206a, 2019
244. RV Listyarini, DS Gesto, P Paiva, MJ Ramos, PA Fernandes, Benchmark of Density Functionals for the Calculation of the Redox potential of Fe3+/Fe2+ within protein coordination shells, Frontiers in Chemistry 7, 391, 2019
245. C Proença, M Freitas, D Ribeiro, SM Tomé, EFT Oliveira, MF Viegas, AN Araújo, MJ Ramos, AMS Silva, PA Fernandes, E Fernandes, Evaluation of a flavonoids library for inhibition of pancreatic α-amylase towards a structure–activity relationship, Journal of Enzyme Inhibition and Medicinal Chemistry 34 (1), 577-588, 2019
246. R Friedman, S Khalid, C Aponte-Santamaría, E Arutyunova, M Becker, ..., Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology, The Journal of Membrane Biology 251 (5-6), 609-631, 2018
247. CD dos Santos Moreira, MJ Ramos, PA Fernandes, Glutamine synthetase structure‐catalysis relationship—Recent advances and applications, Wiley Interdisciplinary Reviews: Computational Molecular Science, e1399, 2018
248. FE Medina, RPP Neves, MJ Ramos, PA Fernandes, QM/MM Study of the Reaction Mechanism of the Dehydratase Domain from Mammalian Fatty Acid Synthase, ACS Catalysis 8 (11), 10267-10278, 2018
249. MJ Ramos, PA Fernandes, Structure, Dynamics, and Energetics of ATP Hydrolysis by ABC Transporters, ACS Central Science 4 (10), 1300-1302, 2018
250. ACC Barbosa, RPP Neves, SF Sousa, MJ Ramos, PA Fernandes, Mechanistic Studies of a Flavin Monooxygenase: Sulfur Oxidation of Dibenzothiophenes by DszC, ACS Catalysis 8 (10), 9298-9311 2, 2018
251. AMN Silva, JTS Coimbra, MM Castro, A Oliveira, NF Bras, PA Fernandes, MJ Ramos, M Rangel, Determining the glycation site specificity of human holo-transferrin, Journal of Inorganic Biochemistry 186, 95-102, 2018
252. NF Brás, PA Fernandes, MJ Ramos, Understanding the Rate‐Limiting Step of Glycogenolysis by Using QM/MM Calculations on Human Glycogen Phosphorylase, ChemMedChem 13 (15), 1608-1616, 2018
253. P Paiva, IPD Costa, CE Ferreira, P Ferreira, AT Pereira, NM Cerqueira, PA Fernandes, MJ Ramos, Studies on neuraminidase inhibition, International Journal of Quantum Chemistry 118 (9), e25592, 2018
254. MA Zúñiga, JB Alderete, GA Jaña, PA Fernandez, MJ Ramos, VA Jiménez, Modulation of lateral and longitudinal interdimeric interactions in microtubule models by Laulimalide and Peloruside A association: A molecular modeling approach on the mechanism of microtubule stabilizing agentes, Chemical Biology & Drug Design 91 (5), 1042-1055, 2018
255. P Paiva, SF Sousa, MJ Ramos, PA Fernandes, Understanding the Catalytic Machinery and the Reaction Pathway of the Malonyl-Acetyl Transferase Domain of Human Fatty Acid Synthase, ACS Catalysis 8 (6), 4860-4872, 2018
256. JR Almeida, B Mendes, M Lancellotti, S Marangoni, N Vale, Ó Passos, MJ Ramos, PA Fernandes, P Gomes, SL aa Silva, A novel synthetic peptide inspired on Lys49 phospholipase A2 from Crotalus oreganus abyssus snake venom active against multidrug-resistant clinical isolates, European Journal of Medicinal Chemistry 149, 248-256, 2018
257. P Ferreira, NM Cerqueira, NF Brás, PA Fernandes, MJ Ramos, Parametrization of molybdenum cofactors for the AMBER force field, Journal of Chemical Theory and Computation 14 (5), 2538-2548, 2018
258. N Cerqueira, PA Fernandes, MJ Ramos, Protocol for computational enzymatic reactivity based on geometry optimisation, ChemPhysChem 19 (6), 669-689, 2018
259. NF Brás, D Santos-Martins, PA Fernandes, MJ Ramos, Mechanistic Pathway on Human α-Glucosidase Maltase-Glucoamylase Unveiled by QM/MM Calculations, The Journal of Physical Chemistry B 122 (14), 3889-3899, 2018
260. D Santos-Martins, AR Calixto, PA Fernandes, MJ Ramos, A Buried Water Molecule Influences Reactivity in α-Amylase on a Subnanosecond Time Scale, ACS Catalysis 8 (5), 4055-4063, 2018
261. NM Cerqueira, PA Fernandes, MJ Ramos, Visualizing the microscopic world, Interdisciplinary Sciences: Computational Life Sciences 10 (1), 105-110, 2018
262. NF Brás, PA Fernandes, MJ Ramos, SD Schwartz, Mechanistic insights on human phosphoglucomutase revealed by transition path sampling and molecular dynamics calculations, Chemistry–A European Journal 24 (8), 1978-1987, 2018
263. MF Viegas, RPP Neves, MJ Ramos, PA Fernandes, Modeling of Human Fatty Acid Synthase and in Silico Docking of Acyl Carrier Protein Domain and Its Partner Catalytic Domains, The Journal of Physical Chemistry B 122 (1), 77-85, 2018
264. JTS Coimbra, NF Brás, PA Fernandes, M Rangel, MJ Ramos, Membrane partition of bis-(3-hydroxy-4-pyridinonato) zinc (ii) complexes revealed by molecular dynamics simulations, RSC Advances 8 (48), 27081-27090, 2018
265. ICM Simões, JTS Coimbra, RPP Neves, IPD Costa, MJ Ramos, ..., Properties that rank protein: protein docking poses with high accuracy, Physical Chemistry Chemical Physics 20 (32), 20927-20942, 2018
266. GA Jaña, F Mendoza, MI Osorio, JB Alderete, PA Fernandes, MJ Ramos, VA Jimenez, A QM/MM approach on the structural and stereoelectronic factors governing glycosylation by GTF-SI from Streptococcus mutans, Organic & Biomolecular Chemistry 16 (14), 2438-2447, 2018
267. C Proença, M Freitas, D Ribeiro, JLC Sousa, F Carvalho, AMS Silva, PA Fernandes, E Fernandes, Inhibition of protein tyrosine phosphatase 1B by flavonoids: A structure-activity relationship study, Food and Chemical Toxicology 111, 474-481, 2018