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8 results in Authors: Bernard Brooks

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

Yalun Yu, Andreas Kramer, Andrew Simmonett, Rick Venable, Alex MacKerell, Jeffery Klauda, Richard W. Pastor, Bernard Brooks

Version 1 posted 30 December 2020

576

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Physical Chemistry

Working Paper

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

Yalun Yu, Andreas Kramer, Rick Venable, Bernard Brooks, Jeffery Klauda, Richard W. Pastor

Version 1 posted 30 December 2020

459

Downloads

Theoretical and Computational Chemistry

Working Paper

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

Daniel Smith, Lori Burns, Andrew Simmonett, Robert Parrish, Matthew Schieber, Raimondas Galvelis, Peter Kraus, Holger Kruse, Roberto Di Remigio, Asem Alenaizan, Andrew James, Susi Lehtola, Jonathon Misiewicz, Maximilian Scheurer, Robert Shaw, Jeffrey Schriber, Yi Xie, Zachary Glick, Dominic Sirianni, Joseph O'Brien, Jonathan Waldrop, Ashutosh Kumar, Edward G. Hohenstein, Benjamin Pritchard, Bernard Brooks, Henry Schaefer, Alexander Sokolov, Konrad Patkowski, Eugene DePrince, Ugur Bozkaya, Rollin King, Francesco Evangelista, Justin Turney, Thomas Crawford, David Sherrill

Version 1 posted 05 March 2020

1,785

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Citations

Theoretical and Computational Chemistry

Working Paper

Efficient and Scalable Electrostatics via Spherical Grids and Treecode Summation

Andrew Simmonett, Bernard Brooks, Thomas Darden

Version 1 posted 02 September 2022

300

Downloads

Citations

Theoretical and Computational Chemistry

Working Paper

Correlation Between Water Molecules Identified in Atomic Models of Beta-Galactosidase Determined by Cryo-EM and X-Ray Crystallography

Florentina Tofoleanu, Lesley Earl, Frank Pickard, Bernard Brooks

Version 1 posted 09 June 2020

771

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Biological and Medicinal Chemistry

Working Paper

Protein pKa prediction by tree-based machine learning

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

Version 1 posted 14 December 2021

702

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Biological and Medicinal Chemistry

Working Paper

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

Richard Van, Xiaoliang Pan, Saadi Rostami, Jin Liu, Pratul Agarwal, Bernard Brooks, Rakhi Rajan, Yihan Shao

Version 1 posted 04 October 2024

194

Downloads

Theoretical and Computational Chemistry

Working Paper

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

Xujian Wang, Junmei Wang, Xiongwu Wu, Bernard Brooks

Version 1 posted 08 November 2024

424

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8 results in Bernard Brooks in Authors: Bernard Brooks

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

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

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

Efficient and Scalable Electrostatics via Spherical Grids and Treecode Summation

Correlation Between Water Molecules Identified in Atomic Models of Beta-Galactosidase Determined by Cryo-EM and X-Ray Crystallography

Protein pKa prediction by tree-based machine learning

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

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

8 results in Authors: Bernard Brooks