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Joćo Vieira Ribeiro
Joćo Vieira Ribeiro
Roivant Discovery
Verified email at roivant.com
Title
Cited by
Cited by
Year
Scalable molecular dynamics on CPU and GPU architectures with NAMD
JC Phillips, DJ Hardy, JDC Maia, JE Stone, JV Ribeiro, RC Bernardi, ...
The Journal of chemical physics 153 (4), 2020
18152020
QwikMD—integrative molecular dynamics toolkit for novices and experts
JV Ribeiro, RC Bernardi, T Rudack, JE Stone, JC Phillips, PL Freddolino, ...
Scientific reports 6 (1), 26536, 2016
1912016
NAMD goes quantum: an integrative suite for hybrid simulations
MCR Melo, RC Bernardi, T Rudack, M Scheurer, C Riplinger, JC Phillips, ...
Nature methods 15 (5), 351-354, 2018
1842018
Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing
JE Stone, M Sener, KL Vandivort, A Barragan, A Singharoy, I Teo, ...
Parallel Computing 55, 17-27, 2016
442016
vsLab—An implementation for virtual high‐throughput screening using AutoDock and VMD
N Cerqueira, J Ribeiro, PA Fernandes, MJ Ramos
International Journal of Quantum Chemistry 111 (6), 1208-1212, 2011
352011
Volarea–a bioinformatics tool to calculate the surface area and the volume of molecular systems
JV Ribeiro, JAC Tamames, NM Cerqueira, PA Fernandes, MJ Ramos
Chemical Biology & Drug Design 82 (6), 743-755, 2013
332013
Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry
T Dixon, D MacPherson, B Mostofian, T Dauzhenka, S Lotz, D McGee, ...
Nature communications 13 (1), 5884, 2022
282022
CompASM: an Amber-VMD alanine scanning mutagenesis plug-in
JV Ribeiro, NM Cerqueira, IS Moreira, PA Fernandes, MJ Ramos
Marco Antonio Chaer Nascimento: A Festschrift from Theoretical Chemistry …, 2014
192014
Atomic-resolution prediction of degrader-mediated ternary complex structures by combining molecular simulations with hydrogen deuterium exchange
T Dixon, D MacPherson, B Mostofian, T Dauzhenka, S Lotz, D McGee, ...
Biorxiv, 2021.09. 26.461830, 2021
122021
QwikMD-gateway for easy simulation with VMD and NAMD
JV Ribeiro, RC Bernardi, T Rudack, K Schulten, E Tajkhorshid
Biophysical Journal 114 (3), 673a-674a, 2018
102018
VMD as a platform for interactive small molecule preparation and visualization in quantum and classical simulations
M Spivak, JE Stone, J Ribeiro, J Saam, PL Freddolino, RC Bernardi, ...
Journal of Chemical Information and Modeling 63 (15), 4664-4678, 2023
82023
chem‐path‐tracker: An Automated Tool to Analyze Chemical Motifs in Molecular Structures
JV Ribeiro, N Cerqueira, PA Fernandes, MJ Ramos
Chemical Biology & Drug Design 84 (1), 44-53, 2014
12014
NAMD 2.13 and beyond: New features, larger systems, and faster GPU simulations
J Maia, D Hardy, B Radak, J Ribeiro, J Stone, E Tajkhorshid
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 258, 2019
2019
Accessible molecular modeling environment with VMD and NAMD
J Ribeiro, E Tajkhorshid
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 258, 2019
2019
QwikMD–easy and fast molecular dynamics simulations with VMD and NAMD
JV Ribeiro, RC Bernardi, T Rudack, K Schulten, E Tajkhorshid
MDPI AG, 2017
2017
Making Classical and Hybrid (QM/MM) Molecular Dynamics Easy and Fast with QwikMD
JV Ribeiro, RC Bernardi, T Rudack, K Schulten
Biophysical Journal 112 (3), 448a, 2017
2017
Easy and Fast Setup of Molecular Dynamics Simulations: Combining VMD and NAMD for Experimentalists
JV Ribeiro, RC Bernardi, T Rudack, K Schulten
Biophysical Journal 110 (3), 641a, 2016
2016
Usage of Poly (NIPAm) in the biofuel production
J Ribeiro, R Bernardi, K Schulten
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 249, 2015
2015
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