Bernard R. Brooks

52 papers Journal 51Unranked 1

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Boltzmann Classifier: A Thermodynamic-Inspired Approach to Supervised Learning. CoRR Muhamed Amin, Bernard R. Brooks
2025	J	`jnl`	Leveraging-Induced Polarization for Drug Discovery: Efficient IC50 Prediction Using Minimal Features. J. Chem. Inf. Model. Ashraf Mohamed, Bernard R. Brooks, Muhamed Amin
2024	J	`jnl`	MPI-parallelization of the grid inhomogeneous solvation theory calculation. J. Comput. Chem. Daniel R. Roe, Bernard R. Brooks
2022	J	`jnl`	GraphVAMPNet, using graph neural networks and variational approach to markov processes for dynamical modeling of biomolecules. CoRR Mahdi Ghorbani, Samarjeet Prasad, Jeffery B. Klauda, Bernard R. Brooks
2022	J	`jnl`	Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches. J. Comput. Aided Mol. Des. Phillip 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
2021	J	`jnl`	A replica exchange umbrella sampling (REUS) approach to predict host-guest binding free energies in SAMPL8 challenge. J. Comput. Aided Mol. Des. Mahdi Ghorbani, Phillip S. Hudson, Michael R. Jones, Félix Aviat, Rubén Meana-Pañeda, Jeffery B. Klauda, Bernard R. Brooks
2021	J	`jnl`	The Extended Eighth-Shell method for periodic boundary conditions with rotational symmetry. J. Comput. Chem. Samarjeet Prasad, Andrew C. Simmonett, Rubén Meana-Pañeda, Bernard R. Brooks
2021	J	`jnl`	Variational embedding of protein folding simulations using gaussian mixture variational autoencoders. CoRR Mahdi Ghorbani, Samarjeet Prasad, Jeffery B. Klauda, Bernard R. Brooks
2020	J	`jnl`	A deep learning approach for the blind logP prediction in SAMPL6 challenge. J. Comput. Aided Mol. Des. Samarjeet Prasad, Bernard R. Brooks
2020	J	`jnl`	Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water-octanol partition coefficients in the SAMPL6 challenge. J. Comput. Aided Mol. Des. Andreas Krämer, Phillip S. Hudson, Michael R. Jones, Bernard R. Brooks
2020	J	`jnl`	Quantum chemical predictions of water-octanol partition coefficients applied to the SAMPL6 logP blind challenge. J. Comput. Aided Mol. Des. Michael R. Jones, Bernard R. Brooks
2020	J	`jnl`	SAMPL6 logP challenge: machine learning and quantum mechanical approaches. J. Comput. Aided Mol. Des. Prajay Patel, David M. Kuntz, Michael R. Jones, Bernard R. Brooks, Angela K. Wilson
2018	J	`jnl`	Absolute and relative pK a predictions via a DFT approach applied to the SAMPL6 blind challenge. J. Comput. Aided Mol. Des. Qiao Zeng, Michael R. Jones, Bernard R. Brooks
2018	J	`jnl`	An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge. J. Comput. Aided Mol. Des. Samarjeet Prasad, Jing Huang, Qiao Zeng, Bernard R. Brooks
2018	J	`jnl`	Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges. J. Comput. Aided Mol. Des. Naohiro Nishikawa, Kyungreem Han, Xiongwu Wu, Florentina Tofoleanu, Bernard R. Brooks
2018	J	`jnl`	Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale. J. Comput. Aided Mol. Des. Phillip S. Hudson, Kyungreem Han, H. Lee Woodcock III, Bernard R. Brooks
2018	J	`jnl`	Prediction of CB[8] host-guest binding free energies in SAMPL6 using the double-decoupling method. J. Comput. Aided Mol. Des. Kyungreem Han, Phillip S. Hudson, Michael R. Jones, Naohiro Nishikawa, Florentina Tofoleanu, Bernard R. Brooks
2017	J	`jnl`	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 challenge. J. Comput. Aided Mol. Des. Florentina Tofoleanu, Juyong Lee, Frank C. Pickard IV, Gerhard König, Jing Huang, Minkyung Baek, Chaok Seok, Bernard R. Brooks
2017	J	`jnl`	Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge. J. Comput. Aided Mol. Des. Juyong Lee, Florentina Tofoleanu, Frank C. Pickard IV, Gerhard König, Jing Huang, Ana Damjanovic, Minkyung Baek, Chaok Seok, Bernard R. Brooks
2017	J	`jnl`	Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level. J. Chem. Inf. Model. Meiting Wang, Pengfei Li, Xiangyu Jia, Wei Liu, Yihan Shao, Wenxin Hu, Jun Zheng, Bernard R. Brooks, Ye Mei
2017	J	`jnl`	OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLoS Comput. Biol. Peter K. 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
2016	J	`jnl`	Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and p J. Comput. Aided Mol. Des. Frank C. Pickard IV, Gerhard König, Florentina Tofoleanu, Juyong Lee, Andrew C. Simmonett, Yihan Shao, Jay W. Ponder, Bernard R. Brooks
2016	J	`jnl`	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 challenge. J. Comput. Aided Mol. Des. Gerhard König, Frank C. Pickard IV, Jing Huang, Andrew C. Simmonett, Florentina Tofoleanu, Juyong Lee, Pavlo O. Dral, Samarjeet Prasad, Michael R. Jones, Yihan Shao, Walter Thiel, Bernard R. Brooks
2016	J	`jnl`	Link community detection through global optimization and the inverse resolution limit of partition density. CoRR Juyong Lee, Zhong-Yuan Zhang, Jooyoung Lee, Bernard R. Brooks, Yong-Yeol Ahn
2016	J	`jnl`	Partition coefficients for the SAMPL5 challenge using transfer free energies. J. Comput. Aided Mol. Des. Michael R. Jones, Bernard R. Brooks, Angela K. Wilson
2016	J	`jnl`	Self-guided Langevin dynamics via generalized Langevin equation. J. Comput. Chem. Xiongwu Wu, Bernard R. Brooks, Eric Vanden-Eijnden
2015	J	`jnl`	A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water. PLoS Comput. Biol. Xiongwu Wu, Bernard R. Brooks
2015	J	`jnl`	Development and implementation of (Q)SAR modeling within the CHARMMing web-user interface. J. Comput. Chem. Iwona E. Weidlich, Yuri Pevzner, Benjamin T. Miller, Igor V. Filippov, H. Lee Woodcock III, Bernard R. Brooks
2015	J	`jnl`	ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites. J. Chem. Inf. Model. Janez Konc, Benjamin T. Miller, Tanja Stular, Samo Lesnik, H. Lee Woodcock III, Bernard R. Brooks, Dusanka Janezic
2015	J	`jnl`	Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest. BMC Bioinform. Juyong Lee, Kiho Lee, InSuk Joung, Keehyoung Joo, Bernard R. Brooks, Jooyoung Lee
2014	J	`jnl`	Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4. J. Comput. Aided Mol. Des. Gerhard König, Frank C. Pickard IV, Ye Mei, Bernard R. Brooks
2014	J	`jnl`	Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial. PLoS Comput. Biol. Benjamin 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
2014	J	`jnl`	Web-Based Computational Chemistry Education with CHARMMing II: Coarse-Grained Protein Folding. PLoS Comput. Biol. Frank C. Pickard IV, Benjamin T. Miller, Vinushka Schalk, Michael G. Lerner, H. Lee Woodcock III, Bernard R. Brooks
2014	J	`jnl`	Web-Based Computational Chemistry Education with CHARMMing III: Reduction Potentials of Electron Transfer Proteins. PLoS Comput. Biol. Bradley Scott Perrin Jr., Benjamin T. Miller, Vinushka Schalk, H. Lee Woodcock III, Bernard R. Brooks, Toshiko Ichiye
2012	J	`jnl`	Comparing normal modes across different models and scales: Hessian reduction J. Comput. Chem. An Ghysels, Benjamin T. Miller, Frank C. Pickard IV, Bernard R. Brooks
2012	J	`jnl`	Correlating Protein Hot Spot Surface Analysis Using ProBiS with Simulated Free Energies of Protein-Protein Interfacial Residues. J. Chem. Inf. Model. Nejc Carl, Milan Hodoscek, Blaz Vehar, Janez Konc, Bernard R. Brooks, Dusanka Janezic
2012	J	`jnl`	Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations. J. Comput. Aided Mol. Des. Gerhard König, Bernard R. Brooks
2012	J	`jnl`	Simulation of multiphase systems utilizing independent force fields to control intraphase and interphase behavior. J. Comput. Chem. Pradip K. Biswas, Nadeem A. Vellore, Jeremy A. Yancey, Tugba G. Kucukkal, Galen Collier, Bernard R. Brooks, Steven J. Stuart, Robert A. Latour
2011	J	`jnl`	The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations. J. Comput. Chem. Urban Borstnik, Benjamin T. Miller, Bernard R. Brooks, Dusanka Janezic
2010	J	`jnl`	Comparative study of various normal mode analysis techniques based on partial Hessians. J. Comput. Chem. An Ghysels, Veronique Van Speybroeck, Ewald Pauwels, Saron Catak, Bernard R. Brooks, Dimitri Van Neck, Michel Waroquier
2009	J	`jnl`	Artificial reaction coordinate "tunneling" in free-energy calculations: The catalytic reaction of RNase H. J. Comput. Chem. Edina Rosta, H. Lee Woodcock III, Bernard R. Brooks, Gerhard Hummer
2009	J	`jnl`	CHARMM: The biomolecular simulation program. J. Comput. Chem. Bernard R. Brooks, Charles L. Brooks III, Alexander D. MacKerell Jr., Lennart Nilsson, Robert J. Petrella, Benoît Roux, Y. Won, G. Archontis, Christian Bartels, Stefan Boresch, Amedeo Caflisch, Leo S. D. Caves, Qiang Cui, Aaron R. Dinner, Michael Feig, S. Fischer, Jiali Gao, Milan Hodoscek, Wonpil Im, Krzysztof Kuczera, Themis Lazaridis, J. Ma, Victor Ovchinnikov, Emanuele Paci, Richard W. Pastor, C. B. Post, J. Z. Pu, Michael Schaefer, Bruce Tidor, Richard M. Venable, H. Lee Woodcock III, X. Wu, W. Yang, Darrin M. York, Martin Karplus
2008	J	`jnl`	CHARMMing: A New, Flexible Web Portal for CHARMM. J. Chem. Inf. Model. Benjamin T. Miller, Rishi P. Singh, Jeffery B. Klauda, Milan Hodoscek, Bernard R. Brooks, H. Lee Woodcock III
2008	J	`jnl`	Open Science Grid Study of the Coupling between Conformation and Water Content in the Interior of a Protein. J. Chem. Inf. Model. Ana Damjanovic, Benjamin T. Miller, Torre J. Wenaus, Petar Maksimovic, Bertrand García-Moreno E., Bernard R. Brooks
2007	J	`jnl`	Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations. J. Comput. Chem. H. Lee Woodcock III, Milan Hodoscek, Andrew T. B. Gilbert, Peter M. W. Gill, Henry F. Schaefer III, Bernard R. Brooks
2007	—	`conf`	Modeling Of Macromolecular Assemblies with Map Objects. BIOCOMP Xiongwu Wu, Bernard R. Brooks
2006	J	`jnl`	Development of small molecules designed to modulate protein-protein interactions. J. Comput. Aided Mol. Des. Ye Che, Bernard R. Brooks, Garland R. Marshall
2004	J	`jnl`	The Local Maximum Clustering Method and Its Application in Microarray Gene Expression Data Analysis. EURASIP J. Adv. Signal Process. Xiongwu Wu, Yidong Chen, Bernard R. Brooks, Yan A. Su
2003	J	`jnl`	An improved method for nonbonded list generation: Rapid determination of near-neighbor pairs. J. Comput. Chem. Robert J. Petrella, Ioan Andricioaei, Bernard R. Brooks, Martin Karplus
1995	J	`jnl`	Harmonic Analysis of Large Systems. I. Methodology. J. Comput. Chem. Bernard R. Brooks, Dusanka Janezic, Martin Karplus
1994	J	`jnl`	A Truncated Newton Minimizer Adapted for CHARMM and Biomolecular Applications. J. Comput. Chem. Philippe Derreumaux, Guihua Zhang, Tamar Schlick, Bernard R. Brooks
1994	J	`jnl`	New Spherical-Cutoff Methods for Long-Range Forces in Macromolecular Simulation. J. Comput. Chem. Peter J. Steinbach, Bernard R. Brooks