| Amber 14 DA Case, V Babin, J Berryman, RM Betz, Q Cai, DS Cerutti, ... University of California, 2014 | 11941* | 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 | 8688* | |
| AMBER 12 DA Case, TA Darden, TE Cheatham III, CL Simmerling, J Wang, RE Duke, ... University of California, San Francisco, 2012 | 8470* | 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 | 5584 | 2013 |
| Amber 2020 DA Case, K Belfon, I Ben-Shalom, SR Brozell, D Cerutti, T Cheatham, ... | 5140 | 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 | 458 | 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 | 289 | 2010 |
| 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 | 237 | 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 | 174 | 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 | 168 | 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 | 167 | 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 | 161 | 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 | 145 | 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 | 141 | 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 | 111 | 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 | 101 | 2018 |
| AmberTools DA Case, HM Aktulga, K Belfon, DS Cerutti, GA Cisneros, VWD Cruzeiro, ... Journal of Chemical Information and Modeling, 2023 | 100 | 2023 |
| 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 | 97 | 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 | 85 | 2014 |
| Reliable Oligonucleotide Conformational Ensemble Generation in Explicit Solvent for Force Field Assessment Using Reservoir Replica Exchange Molecular Dynamics Simulations NM Henriksen, DR Roe, TE Cheatham III The Journal of Physical Chemistry B 117 (15), 4014-4027, 2013 | 70 | 2013 |
Thomas E. Cheatham, IIIProfessor of Medicinal Chemistry; Director Research Computing; University of UtahVerified email at utah.edu
