Thomas E. Cheatham III

16 papers Journal 14Unranked 2
YearRankTypeTitle / Venue / Authors
2025 J jnl
Recent Developments in Amber Biomolecular Simulations.
J. Chem. Inf. Model.
David A. Case, David S. Cerutti, Vinícius Wilian D. Cruzeiro, Thomas A. Darden, Robert E. Duke, Mahdieh Ghazimirsaeed, George M. Giambasu, Timothy J. Giese, Andreas W. Götz, Julie A. Harris, Koushik Kasavajhala, Tai-Sung Lee, Zhen Li, Charles Lin, Jian Liu, Yinglong Miao, Romelia Salomón-Ferrer, Jana Shen, Ryan Snyder, Jason M. Swails, Ross C. Walker, Jinan Wang, Xiongwu Wu, Jinzhe Zeng, Thomas E. Cheatham III, Daniel R. Roe, Adrian E. Roitberg, Carlos Simmerling, Darrin M. York, Maria C. Nagan, Kenneth M. Merz Jr.
2020 — conf
Fostering Collaboration Among Organizations in the Research Computing and Data Ecosystem.
PEARC
Sharon Broude Geva, Dana Brunson, Thomas E. Cheatham III, James Deaton, James Griffioen, Curtis W. Hillegas, Douglas M. Jennewein, Gail Krovitz, Tobin Magle, Patrick Schmitz, Karen Tomko, James C. Wilgenbusch
2018 J jnl
Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data.
J. Comput. Chem.
Daniel R. Roe, Thomas E. Cheatham III
2017 J jnl
Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences.
J. Chem. Inf. Model.
Marie Zgarbová, Petr Jurecka, Filip Lankas, Thomas E. Cheatham III, Jirí Sponer, Michal Otyepka
2016 J jnl
Using Wavelet Analysis To Assist in Identification of Significant Events in Molecular Dynamics Simulations.
J. Chem. Inf. Model.
Zahra Heidari, Daniel R. Roe, Rodrigo Galindo-Murillo, Jahan B. Ghasemi, Thomas E. Cheatham III
2015 J jnl
The Impact of Heterogeneous Computing on Workflows for Biomolecular Simulation and Analysis.
Comput. Sci. Eng.
Thomas E. Cheatham III, Daniel R. Roe
2014 J jnl
Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing.
J. Cheminformatics
Julien C. Thibault, Daniel R. Roe, Julio C. Facelli, Thomas E. Cheatham III
2014 J jnl
Structural and Energetic Analysis of 2-Aminobenzimidazole Inhibitors in Complex with the Hepatitis C Virus IRES RNA Using Molecular Dynamics Simulations.
J. Chem. Inf. Model.
Niel M. Henriksen, Hamed S. Hayatshahi, Darrell R. Davis, Thomas E. Cheatham III
2014 J jnl
iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings.
J. Chem. Inf. Model.
Julien C. Thibault, Thomas E. Cheatham III, Julio C. Facelli
2013 J jnl
iBIOMES: Managing and Sharing Biomolecular Simulation Data in a Distributed Environment.
J. Chem. Inf. Model.
Julien C. Thibault, Julio C. Facelli, Thomas E. Cheatham III
2012 J jnl
Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle.
J. Comput. Chem.
Kiumars Shahrokh, Anita M. Orendt, Garold S. Yost, Thomas E. Cheatham III
2011 — conf
RNA structure refinement and force field evaluation using molecular dynamics simulations.
TG
Niel M. Henriksen, Thomas E. Cheatham III
2006 J jnl
Computational Science and Engineering Online (CSE-Online): A Cyber-Infrastructure for Scientific Computing.
J. Chem. Inf. Model.
Thanh N. Truong, Manohar Nayak, Hung H. Huynh, Tom Cook, Priya Mahajan, Le-Thuy T. Tran, Jannu Bharath, Shrish Jain, Ha B. Pham, Chaiwoot Boonyasiriwat, Nhat Nguyen, Evan Andersen, Yong Kim, Suengkeol Choe, Jihoon Choi, Thomas E. Cheatham III, Julio C. Facelli
2005 J jnl
The Amber biomolecular simulation programs.
J. Comput. Chem.
David A. Case, Thomas E. Cheatham III, Tom Darden, Holger Gohlke, Ray Luo, Kenneth M. Merz Jr., Alexey Onufriev, Carlos Simmerling, Bing Wang, Robert J. Woods
1998 J jnl
The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition.
J. Comput. Chem.
Stephen C. Harvey, Robert K.-Z. Tan, Thomas E. Cheatham III
1997 J jnl
Adventures in Improving the Scaling and Accuracy of a Parallel Molecular Dynamics Program.
J. Supercomput.
Michael F. Crowley, Thomas A. Darden, Thomas E. Cheatham III, David W. Deerfield II