| 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 | 2508 | 2020 |
| 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 | 222 | 2018 |
| 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 | 218 | 2016 |
| 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 | 58 | 2022 |
| 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 | 46 | 2016 |
| VMD as a platform for interactive small molecule preparation and visualization in quantum and classical simulations M Spivak, JE Stone, J Ribeiro, J Saam, L Freddolino, RC Bernardi, ... Journal of chemical information and modeling 63 (15), 4664-4678, 2023 | 41 | 2023 |
| 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 | 36 | 2013 |
| 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 | 35 | 2011 |
| 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 | 25 | 2018 |
| 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 | 19 | 2014 |
| 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 | 13 | 2021 |
| Business models for academic prototypes: A new approach to media innovation L Nyre, J Ribeiro, B Tessem The Journal of Media Innovations (Discontinued) 4 (2), 4-19, 2018 | 4 | 2018 |
| Multirep: Asynchronous multi-device consistency J Ribeiro, J Barreto, P Ferreira Proceedings of the Third International Workshop on Middleware for Pervasive …, 2011 | 3 | 2011 |
| 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 | 1 | 2014 |
| 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 |
Klaus SchultenProfessor of Physics, University of Illinois at Urbana-ChampaignVerified email at ks.uiuc.edu
