João V. Ribeiro

University of Illinois Urbana-Champaign — United States

Biochemistry, Genetics and Molecular Biology · Life Sciences

7h-index3.8kcitations13works0.02yr avg
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Research Topics

Protein Structure and Dynamics(8), Enzyme Structure and Function(4), Protein Degradation and Inhibitors(3), Photosynthetic Processes and Mechanisms(2), RNA and protein synthesis mechanisms(2)

Publications13 total

VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations
Journal of Chemical Information and Modeling·2023· 78 citedOpen Access
Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry
Nature Communications·2022· 93 citedOpen Access
Atomic-Resolution Prediction ofDegrader-mediated Ternary Complex Structuresby Combining Molecular Simulations withHydrogen Deuterium Exchange
2022· 2 citedOpen Access
Atomic-Resolution Prediction of Degrader-mediated Ternary Complex Structures by Combining Molecular Simulations with Hydrogen Deuterium Exchange
2021· 6 citedOpen Access
Scalable molecular dynamics on CPU and GPU architectures with NAMD
The Journal of Chemical Physics·2020· 3.1k citedOpen Access
NAMD goes quantum: an integrative suite for hybrid simulations
Nature Methods·2018· 234 citedOpen Access
QwikMD - Gateway for Easy Simulation with VMD and NAMD
Biophysical Journal·2018· 33 citedOpen Access
QwikMD - easy and fast molecular dynamics simulations with VMD and NAMD
2017Open Access
Making Classical and Hybrid (QM/MM) Molecular Dynamics Easy and Fast with QwikMD
Biophysical Journal·2017Open Access
QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts
Scientific Reports·2016· 232 citedOpen Access
Easy and Fast Setup of Molecular Dynamics Simulations: Combining VMD and NAMD for Experimentalists
Biophysical Journal·2016Open Access
Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing
Parallel Computing·2015· 41 citedOpen Access
Characterization of a novel CBM from Clostridium perfringens
2015

Frequent Co-authors

Rafael C. Bernardi(8), Klaus Schulten(6), Till Rudack(6), John E. Stone(5), J. C. Phillips(4), Emad Tajkhorshid(4), Tom Dixon(3), Derek MacPherson(3), Barmak Mostofian(3), Taras Dauzhenka(3), Samuel Lotz(3), T. Dwight McGee(3), Sharon Shechter(3), Utsab R. Shrestha(3), Rafal Wiewiora(3), Zachary A. McDargh(3), Fen Pei(3), Rajat Kumar Pal(3), Tanner Wilkerson(3), Vipin Sachdeva(3)