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Daniel R. Roe
Daniel R. Roe
Laboratory of Computational Biology, NHLBI, NIH
Verified email at nih.gov
Title
Cited by
Cited by
Year
Amber 14
DA Case, V Babin, J Berryman, RM Betz, Q Cai, DS Cerutti, ...
University of California, 2014
12223*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
8686*
AMBER 12
DA Case, TA Darden, TE Cheatham III, CL Simmerling, J Wang, RE Duke, ...
University of California, San Francisco, 2012
8359*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
54462013
Amber 2020
DA Case, K Belfon, I Ben-Shalom, SR Brozell, D Cerutti, T Cheatham, ...
48592020
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
4452013
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
2872010
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
2272019
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
1742012
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
1672015
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
1632007
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
1542018
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
1412015
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
1402013
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
1052014
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
1002018
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
962007
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
842014
AmberTools
DA Case, HM Aktulga, K Belfon, DS Cerutti, GA Cisneros, VWD Cruzeiro, ...
Journal of Chemical Information and Modeling, 2023
772023
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
702013
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Articles 1–20