| Amber 14 DA Case, V Babin, J Berryman, RM Betz, Q Cai, DS Cerutti, ... University of California, 2014 | 12088* | 2014 |
| AMBER 12; University of California: San Francisco, CA, 2012 DA Case, TA Darden, TE Cheatham III, CL Simmerling, J Wang, RE Duke, ... There is no corresponding record for this reference, 0 | 8806* | |
| AMBER 12 DA Case, TA Darden, TE Cheatham III, CL Simmerling, J Wang, RE Duke, ... University of California, San Francisco, 2012 | 8581* | 2012 |
| PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data DR Roe, TE Cheatham III Journal of Chemical Theory and Computation 9 (7), 3084-3095, 2013 | 6076 | 2013 |
| Amber 2020 DA Case, K Belfon, I Ben-Shalom, SR Brozell, D Cerutti, T Cheatham, ... | 5598 | 2020 |
| Improved Generalized Born Solvent Model Parameters for Protein Simulations H Nguyen, DR Roe, C Simmerling Journal of Chemical Theory and Computation 9 (4), 2020-2034, 2013 | 486 | 2013 |
| Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber T Luchko, S Gusarov, DR Roe, C Simmerling, DA Case, J Tuszynski, ... Journal of chemical theory and computation 6 (3), 607-624, 2010 | 292 | 2010 |
| AmberTools DA Case, HM Aktulga, K Belfon, DS Cerutti, GA Cisneros, VWD Cruzeiro, ... Journal of Chemical Information and Modeling, 2023 | 289 | 2023 |
| Best practices for computing transport properties 1. Self-diffusivity and viscosity from equilibrium molecular dynamics [article v1. 0] EJ Maginn, RA Messerly, DJ Carlson, DR Roe, JR Elliot Living Journal of Computational Molecular Science 1 (1), 6324-6324, 2019 | 266 | 2019 |
| Evaluation of DOCK 6 as a pose generation and database enrichment tool SR Brozell, S Mukherjee, TE Balius, DR Roe, DA Case, RC Rizzo Journal of computer-aided molecular design 26 (6), 749-773, 2012 | 183 | 2012 |
| Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d (GCACGAACGAACGAACGC) R Galindo-Murillo, DR Roe, TE Cheatham III Biochimica et Biophysica Acta (BBA)-General Subjects 1850 (5), 1041-1058, 2015 | 174 | 2015 |
| Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation DR Roe, A Okur, L Wickstrom, V Hornak, C Simmerling The Journal of Physical Chemistry B 111 (7), 1846-1857, 2007 | 168 | 2007 |
| Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v1. 0] A Grossfield, PN Patrone, DR Roe, AJ Schultz, DW Siderius, ... Living journal of computational molecular science 1 (1), 2018 | 167 | 2018 |
| Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields C Bergonzo, NM Henriksen, DR Roe, TE Cheatham RNA 21 (9), 1578-1590, 2015 | 147 | 2015 |
| Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide C Bergonzo, NM Henriksen, DR Roe, JM Swails, AE Roitberg, ... Journal of Chemical Theory and Computation 10 (1), 492-499, 2013 | 143 | 2013 |
| Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics with Hamiltonian Replica Exchange Methods DR Roe, C Bergonzo, TE Cheatham III The Journal of Physical Chemistry B 118 (13), 3543-3552, 2014 | 115 | 2014 |
| Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data DR Roe, TE Cheatham III Journal of computational chemistry 39 (25), 2110-2117, 2018 | 112 | 2018 |
| Improving convergence of replica-exchange simulations through coupling to a high-temperature structure reservoir A Okur, DR Roe, G Cui, V Hornak, C Simmerling Journal of Chemical Theory and Computation 3 (2), 557-568, 2007 | 99 | 2007 |
| On the absence of intrahelical DNA dynamics on the μs to ms timescale R Galindo-Murillo, DR Roe, TE Cheatham III Nature communications 5, 5152, 2014 | 88 | 2014 |
| Self-Tensioning Aquatic Caddisfly Silk: Ca2+-Dependent Structure, Strength, and Load Cycle Hysteresis NN Ashton, DR Roe, RB Weiss, TE Cheatham III, RJ Stewart Biomacromolecules 14 (10), 3668-3681, 2013 | 70 | 2013 |
Thomas E. Cheatham, IIIProfessor of Medicinal Chemistry; Director Research Computing; University of UtahVerified email at utah.edu