Daniel R. Roe

Also affiliated with National Heart Lung and Blood Institute

Biochemistry, Genetics and Molecular BiologyPhysics and AstronomyMaterials Science

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 15 papers. Top paper: “PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data”.

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

Journal of Chemical Theory and Computation(2013)10.1021/ct400341p

N/A

1.3DataRank · unranked

7429 citations

Thomas E. Cheatham, Daniel R. Roe

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

The Journal of Chemical Physics(2020)10.1063/5.0013849

N/A

0DataRank · unranked

107 citations

Bernard R. Brooks, Daniel R. Roe

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

ChemRxiv(2020)10.26434/chemrxiv.13140011.v2

N/A

0DataRank · unranked

4 citations

Anthony Cruz, Daniel R. Roe, Andrew C. Simmonett, Lauren Wickstrom, Nanjie Deng +2 more

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

ChemRxiv(2020)10.26434/chemrxiv.13140011.v1

N/A

0DataRank · unranked

1 citations

Anthony Cruz, Daniel R. Roe, Andrew C. Simmonett, Lauren Wickstrom, Nanjie Deng +2 more

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

Journal of Chemical Theory and Computation(2021)10.1021/acs.jctc.0c01185

N/A

0DataRank · unranked

40 citations

Anthony Cruz, Daniel R. Roe, Andrew C. Simmonett, Lauren Wickstrom, Nanjie Deng +2 more

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

Journal of Molecular Graphics and Modelling(2021)10.1016/j.jmgm.2021.107832

N/A

0DataRank · unranked

12 citations

Bernard R. Brooks, Daniel R. Roe

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

Protein Science(2022)10.1002/pro.4511

N/A

0DataRank · unranked

9 citations

Bernard R. Brooks, Daniel R. Roe

AmberTools

Journal of Chemical Information and Modeling(2023)10.1021/acs.jcim.3c01153

N/A

0DataRank · unranked

1916 citations

Hasan Metin Aktulga, Kellon Belfon, David S. Cerutti, G. Andrés Cisneros, Vinícius Wilian D. Cruzeiro +42 more

MPI‐parallelization of the grid inhomogeneous solvation theory calculation

Journal of Computational Chemistry(2023)10.1002/jcc.27278

N/A

0DataRank · unranked

4 citations

Bernard R. Brooks, Daniel R. Roe

CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed

The Journal of Physical Chemistry B(2024)10.1021/acs.jpcb.4c04100

N/A

0DataRank · unranked

116 citations

Steven L. Austin, Arnaud Blondel, Eric D. Boittier, Stefan Boresch, Matthias Buck +68 more

k-Means NANI: An Improved Clustering Algorithm for Molecular Dynamics Simulations

Journal of Chemical Theory and Computation(2024)10.1021/acs.jctc.4c00308

N/A

0DataRank · unranked

39 citations

Daniel R. Roe, Matthew Kochert, Carlos Simmerling, Ramón Alain Miranda‐Quintana, Lexin Chen

modXNA: A Modular Approach to Parametrization of Modified Nucleic Acids for Use with Amber Force Fields

Journal of Chemical Theory and Computation(2024)10.1021/acs.jctc.4c01164

N/A

0DataRank · unranked

14 citations

Rodrigo Galindo‐Murillo, Daniel R. Roe, Pablo D. Dans, Thomas E. Cheatham, Christina Bergonzo +1 more

Extended Quality (eQual): Radial threshold clustering based on n-ary similarity

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.12.05.627001

N/A

0DataRank · unranked

6 citations

Micah J. Smith, Daniel R. Roe, Ramón Alain Miranda‐Quintana, Lexin Chen

k-Means NANI: an improved clustering algorithm for Molecular Dynamics simulations

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.07.583975

N/A

0DataRank · unranked

3 citations

Daniel R. Roe, Matthew Kochert, Carlos Simmerling, Ramón Alain Miranda‐Quintana, Lexin Chen

Recent Developments in Amber Biomolecular Simulations

Journal of Chemical Information and Modeling(2025)10.1021/acs.jcim.5c01063

N/A

0DataRank · unranked

131 citations

David S. Cerutti, Vinícius Wilian D. Cruzeiro, Thomas A. Darden, Robert E. Duke, Mahdieh Ghazimirsaeed +26 more