D. Roe

发表

Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations.

Niel M. Henriksen, Daniel R Roe, Thomas E Cheatham, 2013, The journal of physical chemistry. B.

Structural basis of pathway-dependent force profiles in stretched DNA.

D. Roe, A. Chaka, 2009, The journal of physical chemistry. B.

Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC).

T. Cheatham, R. Galindo-Murillo, D. Roe, 2015, Biochimica et biophysica acta.

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.

Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory

Andrew C. Simmonett, D. Roe, L. Wickstrom, 2020 .

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.

Best Practices for Computing Transport Properties 1. Self-Diffusivity and Viscosity from Equilibrium Molecular Dynamics [Article v1.0]

J. R. Elliott, Richard A. Messerly, D. Roe, 2019, Living Journal of Computational Molecular Science.

Protonation state of the selectivity filter of bacterial voltage‐gated sodium channels is modulated by ions

B. Brooks, Xiongwu Wu, D. Roe, 2020, Proteins.

Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in GTPase-Associating Center RNA

Hamed S. Hayatshahi, T. Cheatham, K. Hall, 2016, The journal of physical chemistry. B.

Folding cooperativity in a 3-stranded β-sheet model

V. Hornak, C. Simmerling, D. Roe, 2016 .

Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory.

Andrew C. Simmonett, D. Roe, L. Wickstrom, 2020, Journal of chemical theory and computation.

Molecular basis for the broad substrate selectivity of a peptide prenyltransferase

T. Cheatham, D. Roe, S. Nair, 2016, Proceedings of the National Academy of Sciences.

Quantifying the effects of lossy compression on energies calculated from molecular dynamics trajectories

B. Brooks, D. Roe, 2022, Protein science : a publication of the Protein Society.

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data.

Daniel R Roe, Thomas E Cheatham, T. Cheatham, 2013, Journal of chemical theory and computation.

A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations.

Bernard R Brooks, Daniel R Roe, B. Brooks, 2020, The Journal of chemical physics.

Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields

Niel M. Henriksen, Daniel R Roe, Thomas E Cheatham, 2015, RNA.

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.

Improved Generalized Born Solvent Model Parameters for Protein Simulations.

Carlos Simmerling, Hai Nguyen, Daniel R Roe, 2013, Journal of chemical theory and computation.

Self-tensioning aquatic caddisfly silk: Ca2+-dependent structure, strength, and load cycle hysteresis.

Russell J Stewart, Daniel R Roe, Thomas E Cheatham, 2013, Biomacromolecules.

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

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

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.

Improving Convergence of Replica-Exchange Simulations through Coupling to a High-Temperature Structure Reservoir.

Viktor Hornak, Carlos Simmerling, Daniel R Roe, 2007, Journal of chemical theory and computation.

Folding Cooperativity in a Three-stranded β-Sheet Model

V. Hornak, C. Simmerling, D. Roe, 2005 .

Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations

Daniel M. Zuckerman, Andrew J. Schultz, Alan Grossfield, 2018 .

Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v1.0].

Alan Grossfield, Daniel M Zuckerman, Paul N Patrone, 2018, Living journal of computational molecular science.

Improving the speed of volumetric density map generation via cubic spline interpolation.

Bernard R. Brooks, Daniel R. Roe, B. Brooks, 2021, Journal of molecular graphics & modelling.

Evaluation of DOCK 6 as a pose generation and database enrichment tool

Sudipto Mukherjee, David A. Case, Daniel R. Roe, 2012, Journal of Computer-Aided Molecular Design.

Folding cooperativity in a three-stranded beta-sheet model.

V. Hornak, C. Simmerling, D. Roe, 2005, Journal of molecular biology.

Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation.

Lauren Wickstrom, Viktor Hornak, Carlos Simmerling, 2007, The journal of physical chemistry. B.

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.

Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber.

Carlos Simmerling, Andriy Kovalenko, Tyler Luchko, 2010, Journal of chemical theory and computation.

Polyhedral Compilation Support for C++ Features: A Case Study with CPPTRAJ

Mary W. Hall, Thomas Cheatham, Amit Roy, 2017, LCPC.

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..

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

T. Cheatham, D. Roe, 2018, J. Comput. Chem..

Self-tensioning aquatic caddisfly silk: Ca2+-dependent structure, strength, and load cycle hysteresis.

R. Weiss, T. Cheatham, D. Roe, 2013, Biomacromolecules.