Bernard R. Brooks

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 6%percentile

0.231Author DataRank

Indexed papers

1in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 1 indexed paper attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

PKAD-R: Curated, Redesigned and Expanded Database of Experimental pKa Values in Proteins

Journal of Computational Biophysics and Chemistry(2025)10.1142/s2737416525500164

Top 62%

0.231DataRank

Top 62%3 citations

Shailesh Kumar Panday, Kaoru Ri, Emil Alexov, Bernard R. Brooks, A. Damjanović +1 more

Papers

Driven by 51 papers — median percentile 38. Top paper: “CHARMM: A program for macromolecular energy, minimization, and dynamics calculations”.

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

Journal of Computational Chemistry(1983)10.1002/jcc.540040211

N/A

1.4DataRank · unranked

14912 citations

Robert E. Bruccoleri, Barry D. Olafson, David J. States, S. Swaminathan, Martin Karplus +1 more

P SI4 1.4: Open-source software for high-throughput quantum chemistry

The Journal of Chemical Physics(2020)10.1063/5.0006002

N/A

1.0DataRank · unranked

955 citations

Lori A. Burns, Andrew C. Simmonett, Robert M. Parrish, Matthew Cole Schieber, Raimondas Galvelis +30 more

PKAD-R: Curated, Redesigned and Expanded Database of Experimental pKa Values in Proteins

Journal of Computational Biophysics and Chemistry(2025)10.1142/s2737416525500164

Top 62%

0.231DataRank

Top 62%3 citations

Shailesh Kumar Panday, Kaoru Ri, Emil Alexov, Bernard R. Brooks, A. Damjanović +1 more

Critical Sequence Hotspots for Binding of Novel Coronavirus to Angiotensin Converter Enzyme as Evaluated by Molecular Simulations

The Journal of Physical Chemistry B(2020)10.1021/acs.jpcb.0c05994

N/A

0DataRank · unranked

69 citations

Bernard R. Brooks, Jeffery B. Klauda, Mahdi Ghorbani

Quantum chemical predictions of water–octanol partition coefficients applied to the SAMPL6 logP blind challenge

Journal of Computer-Aided Molecular Design(2020)10.1007/s10822-020-00286-1

N/A

0DataRank · unranked

21 citations

Bernard R. Brooks, Michael R. Jones

SAMPL6 logP challenge: machine learning and quantum mechanical approaches

Journal of Computer-Aided Molecular Design(2020)10.1007/s10822-020-00287-0

N/A

0DataRank · unranked

14 citations

David Kuntz, Michael R. Jones, Bernard R. Brooks, Angela K. Wilson, Prajay Patel

Reformulation of the self-guided molecular simulation method

The Journal of Chemical Physics(2020)10.1063/5.0019086

N/A

0DataRank · unranked

8 citations

Bernard R. Brooks, Xiongwu Wu

Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water–octanol partition coefficients in the SAMPL6 challenge

Journal of Computer-Aided Molecular Design(2020)10.1007/s10822-020-00285-2

N/A

0DataRank · unranked

9 citations

Phillip S. Hudson, Michael R. Jones, Bernard R. Brooks, Andreas Krämer

A deep learning approach for the blind logP prediction in SAMPL6 challenge

Journal of Computer-Aided Molecular Design(2020)10.1007/s10822-020-00292-3

N/A

0DataRank · unranked

35 citations

Bernard R. Brooks, Samarjeet Prasad

Psi4 1.4: Open-Source Software for High-Throughput Quantum Chemistry

ChemRxiv(2020)10.26434/chemrxiv.11930031.v1

N/A

0DataRank · unranked

91 citations

Lori A. Burns, Andrew C. Simmonett, Robert M. Parrish, Matthew Schieber, Raimondas Galvelis +30 more

Psi4 1.4: Open-Source Software for High-Throughput Quantum Chemistry

ChemRxiv(2020)10.26434/chemrxiv.11930031

N/A

0DataRank · unranked

32 citations

Lori A. Burns, Andrew C. Simmonett, Robert M. Parrish, Matthew Schieber, Raimondas Galvelis +30 more

Semi-Automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion

ChemRxiv(2020)10.26434/chemrxiv.13480434

N/A

0DataRank · unranked

10 citations

Andreas Krämer, Andrew C. Simmonett, Rick Venable, Alexander D. MacKerell, Jeffery B. Klauda +3 more

Critical Sequence Hot-spots for Binding of nCOV-2019 to ACE2 as Evaluated by Molecular Simulations

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.27.175448

N/A

0DataRank · unranked

9 citations

Bernard R. Brooks, Jeffery B. Klauda, Mahdi Ghorbani

Exploring dynamics and network analysis of spike glycoprotein of SARS-COV-2

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.09.28.317206

N/A

0DataRank · unranked

7 citations

Bernard R. Brooks, Jeffery B. Klauda, Mahdi Ghorbani

CHARMM36 Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for PE, PG, and Ether Lipids

ChemRxiv(2020)10.26434/chemrxiv.13480437.v1

N/A

0DataRank · unranked

0 citations

Andreas Krämer, Rick Venable, Bernard R. Brooks, Jeffery B. Klauda, Richard W. Pastor +1 more

Semi-Automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion

ChemRxiv(2020)10.26434/chemrxiv.13480434.v1

N/A

0DataRank · unranked

0 citations

Andreas Krämer, Andrew C. Simmonett, Rick Venable, Alexander D. MacKerell, Jeffery B. Klauda +3 more

CHARMM36 Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for PE, PG, and Ether Lipids

ChemRxiv(2020)10.26434/chemrxiv.13480437

N/A

0DataRank · unranked

0 citations

Andreas Krämer, Rick Venable, Bernard R. Brooks, Jeffery B. Klauda, Richard W. Pastor +1 more

CHARMM36 Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Phosphatidylethanolamine, Phosphatidylglycerol, and Ether Lipids

Journal of Chemical Theory and Computation(2021)10.1021/acs.jctc.0c01327

N/A

0DataRank · unranked

118 citations

Andreas Krämer, Richard M. Venable, Bernard R. Brooks, Jeffery B. Klauda, Richard W. Pastor +1 more

Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion

Journal of Chemical Theory and Computation(2021)10.1021/acs.jctc.0c01326

N/A

0DataRank · unranked

78 citations

Andreas Krämer, Richard M. Venable, Andrew C. Simmonett, Alexander D. MacKerell, Jeffery B. Klauda +3 more

Exploring dynamics and network analysis of spike glycoprotein of SARS-COV-2

Biophysical Journal(2021)10.1016/j.bpj.2021.02.047

N/A

0DataRank · unranked

29 citations

Bernard R. Brooks, Jeffery B. Klauda, Mahdi Ghorbani

Determinants of conductance of a bacterial voltage-gated sodium channel

Biophysical Journal(2021)10.1016/j.bpj.2021.06.013

N/A

0DataRank · unranked

14 citations

Bernard R. Brooks, A. Damjanović, Ada Y. Chen

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

The Extended Eighth‐Shell method for periodic boundary conditions with rotational symmetry

Journal of Computational Chemistry(2021)10.1002/jcc.26545

N/A

0DataRank · unranked

6 citations

Andrew C. Simmonett, Rubén Meana‐Pañeda, Bernard R. Brooks, Samarjeet Prasad

A replica exchange umbrella sampling (REUS) approach to predict host–guest binding free energies in SAMPL8 challenge

Journal of Computer-Aided Molecular Design(2021)10.1007/s10822-021-00385-7

N/A

0DataRank · unranked

8 citations

Phillip S. Hudson, Michael R. Jones, Félix Aviat, Rubén Meana‐Pañeda, Jeffery B. Klauda +2 more

Protein pKa prediction by tree-based machine learning

ChemRxiv(2021)10.26434/chemrxiv-2021-4d420

N/A

0DataRank · unranked

3 citations

Juyong Lee, Ana Damjanović, Bernard R. Brooks, Ada Y. Chen

Protein p K a Prediction by Tree-Based Machine Learning

Journal of Chemical Theory and Computation(2022)10.1021/acs.jctc.1c01257

N/A

0DataRank · unranked

37 citations

Juyong Lee, Ana Damjanović, Bernard R. Brooks, Ada Y. Chen

Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches

Journal of Computer-Aided Molecular Design(2022)10.1007/s10822-022-00443-8

N/A

0DataRank · unranked

17 citations

Félix Aviat, Rubén Meana‐Pañeda, Luke Warrensford, Benjamin C. Pollard, Samarjeet Prasad +4 more

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

Deep attention based variational autoencoder for antimicrobial peptide discovery

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.08.499340

N/A

0DataRank · unranked

12 citations

Samarjeet Prasad, Bernard R. Brooks, Jeffery B. Klauda, Mahdi Ghorbani

Efficient and Scalable Electrostatics via Spherical Grids and Treecode Summation

ChemRxiv(2022)10.26434/chemrxiv-2022-6xzql

N/A

0DataRank · unranked

2 citations

Bernard R. Brooks, Thomas A. Darden, Andrew C. Simmonett

Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase

Nature Communications(2023)10.1038/s41467-023-37956-1

N/A

0DataRank · unranked

17 citations

Uriel N. Morzan, Florentina Tofoleanu, Aria Gheeraert, Apala Chaudhuri, Gregory W. Kyro +6 more

Ion channel selectivity through ion-modulated changes of selectivity filter p K a values

Proceedings of the National Academy of Sciences(2023)10.1073/pnas.2220343120

N/A

0DataRank · unranked

12 citations

Bernard R. Brooks, A. Damjanović, Ada Y. Chen

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

Exploring CRISPR-Cas9 HNH-Domain-Catalyzed DNA Cleavage Using Accelerated Quantum Mechanical Molecular Mechanical Free Energy Simulation

Biochemistry(2024)10.1021/acs.biochem.4c00651

N/A

0DataRank · unranked

5 citations

Xiaoliang Pan, Saadi Rostami, Jin Liu, Pratul K. Agarwal, Bernard R. Brooks +3 more

An analysis of the structural changes of the oxygen evolving complex of Photosystem II in the S1 and S3 states revealed by serial femtosecond crystallography

Biochimica et Biophysica Acta (BBA) - Bioenergetics(2024)10.1016/j.bbabio.2024.149531

N/A

0DataRank · unranked

5 citations

Jimin Wang, Gary W. Brudvig, M. R. Gunner, Bernard R. Brooks, Muhamed Amin +1 more

Simulating asymmetric membranes using P21 periodic boundary conditions

Methods in enzymology on CD-ROM/Methods in enzymology(2024)10.1016/bs.mie.2024.03.013

N/A

0DataRank · unranked

3 citations

Samarjeet Prasad, Bernard R. Brooks, Richard W. Pastor, Amy Rice

The oxidation of the [4Fe-4S] cluster of DNA primase alters the binding energies with DNA and RNA primers

Biophysical Journal(2024)10.1016/j.bpj.2024.05.007

N/A

0DataRank · unranked

2 citations

Bernard R. Brooks, Muhamed Amin

Exploring CRISPR-Cas9 HNH-Domain Catalyzed DNA Cleavage Using Accelerated Quantum Mechanical Molecular Mechanical Free Energy Simulation

ChemRxiv(2024)10.26434/chemrxiv-2024-kpr4t

N/A

0DataRank · unranked

0 citations

Xiaoliang Pan, Saadi Rostami, Jin Liu, Pratul K. Agarwal, Bernard R. Brooks +3 more

Accurate Free Energy Calculation via Multiscale Simulations Driven by Hybrid Machine Learning and Molecular Mechanics Potentials

Journal of Chemical Theory and Computation(2025)10.1021/acs.jctc.5c00598

N/A

0DataRank · unranked

9 citations

Xiongwu Wu, Bernard R. Brooks, Junmei Wang, Xujian Wang

apoCHARMM: High-performance molecular dynamics simulations on GPUs for advanced simulation methods

The Journal of Chemical Physics(2025)10.1063/5.0264937

N/A

0DataRank · unranked

4 citations

Felix Aviat, James E. Gonzales, Bernard R. Brooks, Samarjeet Prasad

Thermodynamics of arginine interactions with organic phosphates

Biophysical Journal(2025)10.1016/j.bpj.2025.05.019

N/A

0DataRank · unranked

3 citations

Madolyn Britt, Bernard R. Brooks, Sergei Sukharev, Jeffery B. Klauda, Jiyeon Min

A parallel CUDA implementation of the Gauss–Legendre–spherical- t method for electrostatic interactions

The Journal of Chemical Physics(2025)10.1063/5.0264935

N/A

0DataRank · unranked

3 citations

Wonmuk Hwang, Bernard R. Brooks, James E. Gonzales

Self-Guided Molecular Simulation Methods

International Journal of Molecular Sciences(2025)10.3390/ijms262110410

N/A

0DataRank · unranked

1 citations

Bernard R. Brooks, Xiongwu Wu

Gauss–Legendre-spherical- t (GLST) cubature-based factorization of long-range electrostatics in simulations

The Journal of Chemical Physics(2025)10.1063/5.0264936

N/A

0DataRank · unranked

2 citations

James E. Gonzales, Bernard R. Brooks, Wonmuk Hwang

Efficient and scalable electrostatics via spherical grids and treecode summation

The Journal of Chemical Physics(2025)10.1063/5.0264934

N/A

0DataRank · unranked

2 citations

Bernard R. Brooks, Thomas A. Darden, Andrew C. Simmonett

Self-Guided Molecular Simulation to Enhance Concerted Motion

International Journal of Molecular Sciences(2025)10.3390/ijms26051969

N/A

0DataRank · unranked

1 citations

Bernard R. Brooks, Xiongwu Wu

Gauss-Legendre-Spherical-t (GLST) Cubature-Based Factorization of Long-Range Electrostatics in Simulations

ChemRxiv(2025)10.26434/chemrxiv-2025-q8q77

N/A

0DataRank · unranked

0 citations

James E. Gonzales, Bernard R. Brooks, Wonmuk Hwang

A Parallel CUDA Implementation of the Gauss-Legendre-Spherical-t Method for Electrostatic Interactions

ChemRxiv(2025)10.26434/chemrxiv-2025-904ch

N/A

0DataRank · unranked

0 citations

Wonmuk Hwang, Bernard R. Brooks, James E. Gonzales

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

Membrane permeability of small molecules from unbiased molecular dynamics simulations

The Journal of Chemical Physics(2020)10.1063/5.0013429

N/A

0DataRank · unranked

71 citations

An Ghysels, Eric Wang, Richard M. Venable, Jeffery B. Klauda, Bernard R. Brooks +2 more

Bernard R. Brooks

Indexed papers

Top data-sharing exemplar

Papers