Bernard R. Brooks - researchr alias

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Viewing Publication 1 - 45 from 45

2024

MPI-parallelization of the grid inhomogeneous solvation theory calculationDaniel R. Roe, Bernard R. Brooks. jcc, 45(10):633-637, April 2024. [doi]

2022

Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approachesPhillip S. Hudson, Félix Aviat, Rubén Meana-Pañeda, Luke C. Warrensford, Benjamin C. Pollard, Samarjeet Prasad, Michael R. Jones, H. Lee Woodcock III, Bernard R. Brooks. jcamd, 36(4):263-277, 2022. [doi]

2021

A replica exchange umbrella sampling (REUS) approach to predict host-guest binding free energies in SAMPL8 challengeMahdi Ghorbani, Phillip S. Hudson, Michael R. Jones, Félix Aviat, Rubén Meana-Pañeda, Jeffery B. Klauda, Bernard R. Brooks. jcamd, 35(5):667-677, 2021. [doi]

The Extended Eighth-Shell method for periodic boundary conditions with rotational symmetrySamarjeet Prasad, Andrew C. Simmonett, Rubén Meana-Pañeda, Bernard R. Brooks. jcc, 42(19):1373-1383, 2021. [doi]

2020

2018

Prediction of CB[8] host-guest binding free energies in SAMPL6 using the double-decoupling methodKyungreem Han, Phillip S. Hudson, Michael R. Jones, Naohiro Nishikawa, Florentina Tofoleanu, Bernard R. Brooks. jcamd, 32(10):1059-1073, 2018. [doi]

Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary talePhillip S. Hudson, Kyungreem Han, H. Lee Woodcock III, Bernard R. Brooks. jcamd, 32(10):983-999, 2018. [doi]

Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challengesNaohiro Nishikawa, Kyungreem Han, Xiongwu Wu, Florentina Tofoleanu, Bernard R. Brooks. jcamd, 32(10):1075-1086, 2018. [doi]

An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challengeSamarjeet Prasad, Jing Huang 0004, Qiao Zeng, Bernard R. Brooks. jcamd, 32(10):1191-1201, 2018. [doi]

Absolute and relative pK a predictions via a DFT approach applied to the SAMPL6 blind challengeQiao Zeng, Michael R. Jones, Bernard R. Brooks. jcamd, 32(10):1179-1189, 2018. [doi]

2017

OpenMM 7: Rapid development of high performance algorithms for molecular dynamicsPeter Eastman, Jason M. Swails, John D. Chodera, Robert McGibbon, Yutong Zhao, Kyle Beauchamp, Lee-Ping Wang, Andrew C. Simmonett, Matthew P. Harrigan, Chaya D. Stern, Rafal P. Wiewiora, Bernard R. Brooks, Vijay S. Pande. ploscb, 13(7), 2017. [doi]

Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challengeJuyong Lee, Florentina Tofoleanu, Frank C. Pickard IV, Gerhard König, Jing Huang, Ana Damjanovic, Minkyung Baek, Chaok Seok, Bernard R. Brooks. jcamd, 31(1):71-85, 2017. [doi]

Absolute binding free energies for octa-acids and guests in SAMPL5 - Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challengeFlorentina Tofoleanu, Juyong Lee, Frank C. Pickard IV, Gerhard König, Jing Huang, Minkyung Baek, Chaok Seok, Bernard R. Brooks. jcamd, 31(1):107-118, 2017. [doi]

Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical LevelMeiting Wang, Pengfei Li, Xiangyu Jia, Wei Liu, Yihan Shao, Wenxin Hu, Jun Zheng, Bernard R. Brooks, Ye Mei. jcisd, 57(10):2476-2489, October 2017. [doi]

2016

a correctionsFrank C. Pickard IV, Gerhard König, Florentina Tofoleanu, Juyong Lee, Andrew C. Simmonett, Yihan Shao, Jay W. Ponder, Bernard R. Brooks. jcamd, 30(11):1087-1100, 2016. [doi]

Partition coefficients for the SAMPL5 challenge using transfer free energiesMichael R. Jones, Bernard R. Brooks, Angela K. Wilson. jcamd, 30(11):1129-1138, 2016. [doi]

Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challengeGerhard König, Frank C. Pickard IV, Jing Huang, Andrew C. Simmonett, Florentina Tofoleanu, Juyong Lee, Pavlo O. Dral, Samarjeet Prasad, Michael Jones, Yihan Shao, Walter Thiel, Bernard R. Brooks. jcamd, 30(11):989-1006, 2016. [doi]

Self-guided Langevin dynamics via generalized Langevin equationXiongwu Wu, Bernard R. Brooks, Eric Vanden-Eijnden. jcc, 37(6):595-601, 2016. [doi]

2015

ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding SitesJanez Konc, Benjamin T. Miller, Tanja Stular, Samo Lesnik, H. Lee Woodcock III, Bernard R. Brooks, Dusanka Janezic. jcisd, 55(11):2308-2314, 2015. [doi]

Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forestJuyong Lee, Kiho Lee, InSuk Joung, Keehyoung Joo, Bernard R. Brooks, Jooyoung Lee. bmcbi, 16:94, 2015. [doi]

Development and implementation of (Q)SAR modeling within the CHARMMing web-user interfaceIwona E. Weidlich, Yuri Pevzner, Benjamin T. Miller, Igor V. Filippov, H. Lee Woodcock III, Bernard R. Brooks. jcc, 36(1):62-67, 2015. [doi]

A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit WaterXiongwu Wu, Bernard R. Brooks. ploscb, 11(10), 2015. [doi]

2014

Web-Based Computational Chemistry Education with CHARMMing II: Coarse-Grained Protein FoldingFrank C. Pickard IV, Benjamin T. Miller, Vinushka Schalk, Michael G. Lerner, H. Lee Woodcock III, Bernard R. Brooks. ploscb, 10(7), 2014. [doi]

Web-Based Computational Chemistry Education with CHARMMing III: Reduction Potentials of Electron Transfer ProteinsBradley Scott Perrin Jr., Benjamin T. Miller, Vinushka Schalk, H. Lee Woodcock III, Bernard R. Brooks, Toshiko Ichiye. ploscb, 10(7), 2014. [doi]

Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4Gerhard König, Frank C. Pickard IV, Ye Mei, Bernard R. Brooks. jcamd, 28(3):245-257, 2014. [doi]

Web-Based Computational Chemistry Education with CHARMMing I: Lessons and TutorialBenjamin T. Miller, Rishi P. Singh, Vinushka Schalk, Yuri Pevzner, Jingjun Sun, Carrie S. Miller, Stefan Boresch, Toshiko Ichiye, Bernard R. Brooks, H. Lee Woodcock III. ploscb, 10(7), 2014. [doi]

2012

Simulation of multiphase systems utilizing independent force fields to control intraphase and interphase behaviorPradip K. Biswas, Nadeem A. Vellore, Jeremy A. Yancey, Tugba G. Kucukkal, Galen Collier, Bernard R. Brooks, Steven J. Stuart, Robert A. Latour. jcc, 33(16):1458-1466, 2012. [doi]

Correlating Protein Hot Spot Surface Analysis Using ProBiS with Simulated Free Energies of Protein-Protein Interfacial ResiduesNejc Carl, Milan Hodoscek, Blaz Vehar, Janez Konc, Bernard R. Brooks, Dusanka Janezic. jcisd, 52(10):2541-2549, 2012. [doi]

versus coarse-grainingAn Ghysels, Benjamin T. Miller, Frank C. Pickard IV, Bernard R. Brooks. jcc, 33(28):2250-2275, 2012. [doi]

Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculationsGerhard König, Bernard R. Brooks. jcamd, 26(5):543-550, 2012. [doi]

2011

The distributed diagonal force decomposition method for parallelizing molecular dynamics simulationsUrban Borstnik, Benjamin T. Miller, Bernard R. Brooks, Dusanka Janezic. jcc, 32(14):3005-3013, 2011. [doi]

2010

Comparative study of various normal mode analysis techniques based on partial HessiansAn Ghysels, Veronique Van Speybroeck, Ewald Pauwels, Saron Catak, Bernard R. Brooks, Dimitri Van Neck, Michel Waroquier. jcc, 31(5):994-1007, 2010. [doi]

2009

2008

Open Science Grid Study of the Coupling between Conformation and Water Content in the Interior of a ProteinAna Damjanovic, Benjamin T. Miller, Torre J. Wenaus, Petar Maksimovic, Bertrand García-Moreno E., Bernard R. Brooks. jcisd, 48(10):2021-2029, 2008. [doi]

CHARMMing: A New, Flexible Web Portal for CHARMMBenjamin T. Miller, Rishi P. Singh, Jeffery B. Klauda, Milan Hodoscek, Bernard R. Brooks, H. Lee Woodcock III. jcisd, 48(9):1920-1929, 2008. [doi]

2007

Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculationsH. Lee Woodcock III, Milan Hodoscek, Andrew T. B. Gilbert, Peter M. W. Gill, Henry F. Schaefer III, Bernard R. Brooks. jcc, 28(9):1485-1502, 2007. [doi]

2006

Development of small molecules designed to modulate protein-protein interactionsYe Che, Bernard R. Brooks, Garland R. Marshall. jcamd, 20(2):109-130, 2006. [doi]

2004

The Local Maximum Clustering Method and Its Application in Microarray Gene Expression Data AnalysisXiongwu Wu, Yidong Chen, Bernard R. Brooks, Yan A. Su. ejasp, 2004(1):53-63, 2004. [doi]

1995

Harmonic Analysis of Large Systems. I. MethodologyBernard R. Brooks, Dusanka Janezic, Martin Karplus. jcc, 16(12):1522-1542, 1995.

1994

A Truncated Newton Minimizer Adapted for CHARMM and Biomolecular ApplicationsPhilippe Derreumaux, Guhua Zhang, Tamar Schlick, Bernard R. Brooks. jcc, 15(5):532-552, 1994.

New Spherical-Cutoff Methods for Long-Range Forces in Macromolecular SimulationPeter J. Steinbach, Bernard R. Brooks. jcc, 15(7):667-683, 1994.

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