Thomas E. Cheatham

发表

Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing

Julio C. Facelli, Julien C. Thibault, Daniel R. Roe, 2014, Journal of Cheminformatics.

Molecular dynamics simulations using particle-mesh ewald methods

Michael F. Crowley, Thomas E. Cheatham, David W. Deerfield, 1999 .

Adventures in Improving the Scaling and Accuracy of a Parallel Molecular Dynamics Program

Thomas A. Darden, Michael Crowley, Thomas E. Cheatham, 1997, The Journal of Supercomputing.

The Amber biomolecular simulation programs

Holger Gohlke, Ray Luo, Bing Wang, 2005, J. Comput. Chem..

iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings

Julio C. Facelli, Julien C. Thibault, Thomas E. Cheatham, 2014, J. Chem. Inf. Model..

Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences

Michal Otyepka, Thomas E. Cheatham, Jirí Sponer, 2017, J. Chem. Inf. Model..

Computational Science and Engineering Online (CSE-Online): A Cyber-Infrastructure for Scientific Computing

Yong Kim, Julio C. Facelli, Jihoon Choi, 2006, J. Chem. Inf. Model..

The Impact of Heterogeneous Computing on Workflows for Biomolecular Simulation and Analysis

Daniel R. Roe, Thomas E. Cheatham, T. Cheatham, 2015, Computing in Science & Engineering.

Structural and Energetic Analysis of 2-Aminobenzimidazole Inhibitors in Complex with the Hepatitis C Virus IRES RNA Using Molecular Dynamics Simulations

Niel M. Henriksen, Thomas E. Cheatham, Hamed S. Hayatshahi, 2014, J. Chem. Inf. Model..

Using Wavelet Analysis To Assist in Identification of Significant Events in Molecular Dynamics Simulations

Daniel R. Roe, Thomas E. Cheatham, Jahan B. Ghasemi, 2016, J. Chem. Inf. Model..

Ensembles of AMBER biomolecular simulations on GPUs for assessment and validation of RNA models

Thomas E. Cheatham, 2014 .

The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition

Thomas E. Cheatham, Stephen C. Harvey, Robert K.-Z. Tan, 1998, J. Comput. Chem..

Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data

Daniel R. Roe, Thomas E. Cheatham, T. Cheatham, 2018, J. Comput. Chem..

iBIOMES: Managing and Sharing Biomolecular Simulation Data in a Distributed Environment

Julio C. Facelli, Julien C. Thibault, Thomas E. Cheatham, 2013, J. Chem. Inf. Model..

Quantum mechanically derived AMBER‐compatible heme parameters for various states of the cytochrome P450 catalytic cycle

Thomas E. Cheatham, Anita M. Orendt, Kiumars Shahrokh, 2012, J. Comput. Chem..

Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide

Adrian E. Roitberg, Niel M. Henriksen, Daniel R. Roe, 2013, Journal of chemical theory and computation.

AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules

Peter A. Kollman, David A. Case, David A. Pearlman, 1995 .

Chapter 6 Molecular Modeling and Atomistic Simulation of Nucleic Acids

Thomas E. Cheatham, T. Cheatham, 2005 .

Consensus Conformations of Dinucleoside Monophosphates Described with Well-Converged Molecular Dynamics Simulations.

Niel M. Henriksen, Thomas E. Cheatham, Hamed S. Hayatshahi, 2018, Journal of chemical theory and computation.

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins.

Michal Otyepka, Modesto Orozco, Thomas E. Cheatham, 2010, Journal of chemical theory and computation.

Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters

Thomas E. Cheatham, T. Cheatham, InSuk Joung, 2009, The journal of physical chemistry. B.

Particle-Mesh Based Methods for Fast Ewald Summation in Molecular Dynamics Simulations

Thomas E. Cheatham, Thomas A. Darden, Lee G. Pedersen, 1997, PPSC.

Molecular Dynamics Simulation of Nucleic Acids

Peter A. Kollman, Thomas E. Cheatham, P. Kollman, 2001 .

Molecular dynamics simulations highlight the structural differences among DNA: DNA, RNA:RNA, and DNA:RNA hybrid duplexes

Peter A. Kollman, Thomas E. Cheatham, P. Kollman, 1997 .

Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics with Hamiltonian Replica Exchange Methods

Daniel R. Roe, Thomas E. Cheatham, Christina Bergonzo, 2014, The journal of physical chemistry. B.

Removal of pressure and free energy artifacts in charged periodic systems via net charge corrections to the Ewald potential

Bernard R. Brooks, Thomas E. Cheatham, B. Brooks, 1998 .

On the absence of intra-helical DNA dynamics on the µs to ms timescale

Daniel R. Roe, Thomas E. Cheatham, Rodrigo Galindo-Murillo, 2014, Nature Communications.

Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations

Jaroslav Koča, Thomas E. Cheatham, Jiří Šponer, 2013, Nucleic acids research.

Amber 2015, University of California, San Francisco

Holger Gohlke, Ray Luo, Adrian E. Roitberg, 2015 .

Molecular Dynamics Simulations on Nucleic Acid Systems Using the Cornell et al. Force Field and Particle Mesh Ewald Electrostatics

Peter A. Kollman, Piotr Cieplak, Thomas E. Cheatham, 1998 .