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Paulo Ricardo Batista
Paulo Ricardo Batista
Programa de Computação Científica, Fundação Oswaldo Cruz
Verified email at fiocruz.br
Title
Cited by
Cited by
Year
Exploring free energy landscapes of large conformational changes: molecular dynamics with excited normal modes
MGS Costa, PR Batista, PM Bisch, D Perahia
Journal of chemical theory and computation 11 (6), 2755-2767, 2015
592015
Automated structure modeling of large protein assemblies using crosslinks as distance restraints
M Ferber, J Kosinski, A Ori, UJ Rashid, M Moreno-Morcillo, B Simon, ...
Nature methods 13 (6), 515-520, 2016
562016
Molecular dynamics simulations applied to the study of subtypes of HIV-1 protease common to Brazil, Africa, and Asia
PR Batista, A Wilter, EHAB Durham, PG Pascutti
Cell biochemistry and biophysics 44, 395-404, 2006
522006
High temperatures enhance cooperative motions between CBM and catalytic domains of a thermostable cellulase: mechanism insights from essential dynamics
PR Batista, MG de Souza Costa, PG Pascutti, PM Bisch, W de Souza
Physical Chemistry Chemical Physics 13 (30), 13709-13720, 2011
442011
Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis—application to the HIV-1 protease
PR Batista, CH Robert, JD Marechal, MB Hamida-Rebaï, PG Pascutti, ...
Physical Chemistry Chemical Physics 12 (12), 2850-2859, 2010
402010
Free energy profiles along consensus normal modes provide insight into HIV-1 protease flap opening
PR Batista, G Pandey, PG Pascutti, PM Bisch, D Perahia, CH Robert
Journal of chemical theory and computation 7 (8), 2348-2352, 2011
392011
How does heparin prevent the pH inactivation of cathepsin B? Allosteric mechanism elucidated by docking and molecular dynamics
MGS Costa, PR Batista, CS Shida, CH Robert, PM Bisch, PG Pascutti
BMC genomics 11 (5), S5, 2010
342010
Interplay between parasite cysteine proteases and the host kinin system modulates microvascular leakage and macrophage infection by promastigotes of the Leishmania donovani complex
E Svensjö, PR Batista, CI Brodskyn, R Silva, APCA Lima, V Schmitz, ...
Microbes and infection 8 (1), 206-220, 2006
322006
Understanding the HIV-1 protease nelfinavir resistance mutation D30N in subtypes B and C through molecular dynamics simulations
RO Soares, PR Batista, MGS Costa, LE Dardenne, PG Pascutti, ...
Journal of Molecular Graphics and Modelling 29 (2), 137-147, 2010
302010
Conformational Equilibrium of CDK/Cyclin Complexes by Molecular Dynamics with Excited Normal Modes
N Floquet, MGS Costa, PR Batista, P Renault, PM Bisch, F Raussin, ...
Biophysical journal 109 (6), 1179-1189, 2015
292015
Design, docking studies and molecular dynamics of new potential selective inhibitors of Plasmodium falciparum serine hydroxymethyltransferase
ML da Silva, A da Silva Gonçalves, P Ricardo Batista, JD Figueroa-Villar, ...
Molecular Simulation 36 (1), 5-14, 2010
252010
Predicting functional residues in Plasmodium falciparum plasmepsins by combining sequence and structural analysis with molecular dynamics simulations
PA Valiente, PR Batista, A Pupo, T Pons, A Valencia, PG Pascutti
Proteins: Structure, Function, and Bioinformatics 73 (2), 440-457, 2008
252008
Exploring the unbinding of Leishmania (L.) amazonensis CPB derived‐epitopes from H2 MHC class I proteins
AML Brandt, PR Batista, F Souza‐Silva, CR Alves, ER Caffarena
Proteins: Structure, Function, and Bioinformatics 84 (4), 473-487, 2016
222016
New parameterization approaches of the LIE method to improve free energy calculations of PlmII‐Inhibitors complexes
PA Valiente, A Gil L, PR Batista, ER Caffarena, T Pons, PG Pascutti
Journal of computational chemistry 31 (15), 2723-2734, 2010
192010
Gallic acid modulates phenotypic behavior and gene expression in oral squamous cell carcinoma cells by interfering with leptin pathway
EMS Santos, RG da Rocha, HO Santos, TA Guimarães, ...
Pathology-Research and Practice 214 (1), 30-37, 2018
142018
Gedunin binds to myeloid differentiation protein 2 and impairs lipopolysaccharide-induced toll-like receptor 4 signaling in macrophages
PV Borges, KH Moret, CM Maya-Monteiro, F Souza-Silva, CR Alves, ...
Molecular pharmacology 88 (5), 949-961, 2015
142015
Impact of M36I polymorphism on the interaction of HIV-1 protease with its substrates: insights from molecular dynamics
MGS Costa, TG Benetti-Barbosa, N Desdouits, A Blondel, PM Bisch, ...
BMC genomics 15 (7), S5, 2014
142014
Computational engineering of cellulase Cel9A-68 functional motions through mutations in its linker region
MGS Costa, YF Silva, PR Batista
Physical Chemistry Chemical Physics 20 (11), 7643-7652, 2018
122018
Molecular dynamics simulations of peptide inhibitors complexed with Trypanosoma cruzi Trypanothione reductase
SS Da Rocha Pita, PR Batista, MG Albuquerque, PG Pascutti
Chemical biology & drug design 80 (4), 561-571, 2012
122012
Glycosylation effects on the structure and dynamics of a full-length Cel7A cellulase
CE Pena Jr, MGS Costa, PR Batista
Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 1868 (1), 140248, 2020
82020
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