A Truncated Newton Minimizer Adapted for CHARMM and Biomolecular Applications. - Philippe Derreumaux; Guihua Zhang; Tamar Schlick; Bernard R. Brooks (J. Comput. Chem., 1994)

New Spherical-Cutoff Methods for Long-Range Forces in Macromolecular Simulation. - Peter J. Steinbach; Bernard R. Brooks (J. Comput. Chem., 1994)

Harmonic Analysis of Large Systems. I. Methodology. - Bernard R. Brooks; Dusanka Janezic; Martin Karplus (J. Comput. Chem., 1995)

An improved method for nonbonded list generation: Rapid determination of near-neighbor pairs. - Robert J. Petrella; Ioan Andricioaei; Bernard R. Brooks; Martin Karplus (J. Comput. Chem., 2003)

The Local Maximum Clustering Method and Its Application in Microarray Gene Expression Data Analysis. - Xiongwu Wu; Yidong Chen 002; Bernard R. Brooks; Yan A. Su (EURASIP J. Adv. Signal Process., 2004)

Development of small molecules designed to modulate protein-protein interactions. - Ye Che; Bernard R. Brooks; Garland R. Marshall (J. Comput. Aided Mol. Des., 2006)

Modeling Of Macromolecular Assemblies with Map Objects. - Xiongwu Wu; Bernard R. Brooks (BIOCOMP, 2007)

Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations. - H. Lee Woodcock III; Milan Hodoscek; Andrew T. B. Gilbert; Peter M. W. Gill; Henry F. Schaefer III; Bernard R. Brooks (J. Comput. Chem., 2007)

Open Science Grid Study of the Coupling between Conformation and Water Content in the Interior of a Protein. - Ana Damjanovic; Benjamin T. Miller; Torre J. Wenaus; Petar Maksimovic; Bertrand García-Moreno E.; Bernard R. Brooks (J. Chem. Inf. Model., 2008)

CHARMMing: A New, Flexible Web Portal for CHARMM. - Benjamin T. Miller; Rishi P. Singh; Jeffery B. Klauda; Milan Hodoscek; Bernard R. Brooks; H. Lee Woodcock III (J. Chem. Inf. Model., 2008)

CHARMM: The biomolecular simulation program. - 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; et al. (J. Comput. Chem., 2009)

Artificial reaction coordinate "tunneling" in free-energy calculations: The catalytic reaction of RNase H. - Edina Rosta; H. Lee Woodcock III; Bernard R. Brooks; Gerhard Hummer (J. Comput. Chem., 2009)

Comparative study of various normal mode analysis techniques based on partial Hessians. - An Ghysels; Veronique Van Speybroeck; Ewald Pauwels; Saron Catak; Bernard R. Brooks; Dimitri Van Neck; Michel Waroquier (J. Comput. Chem., 2010)

The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations. - Urban Borstnik; Benjamin T. Miller; Bernard R. Brooks; Dusanka Janezic (J. Comput. Chem., 2011)

Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations. - Gerhard König; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2012)

Simulation of multiphase systems utilizing independent force fields to control intraphase and interphase behavior. - Pradip K. Biswas; Nadeem A. Vellore; Jeremy A. Yancey; Tugba G. Kucukkal; Galen Collier; Bernard R. Brooks; Steven J. Stuart; Robert A. Latour (J. Comput. Chem., 2012)

Comparing normal modes across different models and scales: Hessian reduction versus coarse-graining. - An Ghysels; Benjamin T. Miller; Frank C. Pickard IV; Bernard R. Brooks (J. Comput. Chem., 2012)

Correlating Protein Hot Spot Surface Analysis Using ProBiS with Simulated Free Energies of Protein-Protein Interfacial Residues. - Nejc Carl; Milan Hodoscek; Blaz Vehar; Janez Konc; Bernard R. Brooks; Dusanka Janezic (J. Chem. Inf. Model., 2012)

Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4. - Gerhard König; Frank C. Pickard IV; Ye Mei; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2014)

Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial. - 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 (PLoS Comput. Biol., 2014)

Web-Based Computational Chemistry Education with CHARMMing III: Reduction Potentials of Electron Transfer Proteins. - Bradley Scott Perrin Jr.; Benjamin T. Miller; Vinushka Schalk; H. Lee Woodcock III; Bernard R. Brooks; Toshiko Ichiye (PLoS Comput. Biol., 2014)

Web-Based Computational Chemistry Education with CHARMMing II: Coarse-Grained Protein Folding. - Frank C. Pickard IV; Benjamin T. Miller; Vinushka Schalk; Michael G. Lerner; H. Lee Woodcock III; Bernard R. Brooks (PLoS Comput. Biol., 2014)

Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest. - Juyong Lee; Kiho Lee; InSuk Joung; Keehyoung Joo; Bernard R. Brooks; Jooyoung Lee 002 (BMC Bioinform., 2015)

Development and implementation of (Q)SAR modeling within the CHARMMing web-user interface. - Iwona E. Weidlich; Yuri Pevzner; Benjamin T. Miller; Igor V. Filippov; H. Lee Woodcock III; Bernard R. Brooks (J. Comput. Chem., 2015)

ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites. - Janez Konc; Benjamin T. Miller; Tanja Stular; Samo Lesnik; H. Lee Woodcock III; Bernard R. Brooks; Dusanka Janezic (J. Chem. Inf. Model., 2015)

A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water. - Xiongwu Wu; Bernard R. Brooks (PLoS Comput. Biol., 2015)

Link community detection through global optimization and the inverse resolution limit of partition density. - Juyong Lee; Zhong-Yuan Zhang; Jooyoung Lee 002; Bernard R. Brooks; Yong-Yeol Ahn (CoRR, 2016)

Partition coefficients for the SAMPL5 challenge using transfer free energies. - Michael R. Jones; Bernard R. Brooks; Angela K. Wilson (J. Comput. Aided Mol. Des., 2016)

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. - Gerhard König; Frank C. Pickard IV; Jing Huang 004; Andrew C. Simmonett; Florentina Tofoleanu; Juyong Lee; Pavlo O. Dral; Samarjeet Prasad; Michael R. Jones; Yihan Shao; Walter Thiel; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2016)

Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections. - Frank C. Pickard IV; Gerhard König; Florentina Tofoleanu; Juyong Lee; Andrew C. Simmonett; Yihan Shao; Jay W. Ponder; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2016)

Self-guided Langevin dynamics via generalized Langevin equation. - Xiongwu Wu; Bernard R. Brooks; Eric Vanden-Eijnden (J. Comput. Chem., 2016)

Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge. - Juyong Lee; Florentina Tofoleanu; Frank C. Pickard IV; Gerhard König; Jing Huang 004; Ana Damjanovic; Minkyung Baek; Chaok Seok; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2017)

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. - Florentina Tofoleanu; Juyong Lee; Frank C. Pickard IV; Gerhard König; Jing Huang 004; Minkyung Baek; Chaok Seok; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2017)

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. - 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; et al. (PLoS Comput. Biol., 2017)

Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level. - Meiting Wang; Pengfei Li; Xiangyu Jia; Wei Liu; Yihan Shao; Wenxin Hu; Jun Zheng; Bernard R. Brooks; Ye Mei (J. Chem. Inf. Model., 2017)

Prediction of CB[8] host-guest binding free energies in SAMPL6 using the double-decoupling method. - Kyungreem Han; Phillip S. Hudson; Michael R. Jones; Naohiro Nishikawa; Florentina Tofoleanu; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2018)

Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale. - Phillip S. Hudson; Kyungreem Han; H. Lee Woodcock III; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2018)

Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges. - Naohiro Nishikawa; Kyungreem Han; Xiongwu Wu; Florentina Tofoleanu; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2018)

An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge. - Samarjeet Prasad; Jing Huang 004; Qiao Zeng; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2018)

Absolute and relative pK a predictions via a DFT approach applied to the SAMPL6 blind challenge. - Qiao Zeng; Michael R. Jones; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2018)

Quantum chemical predictions of water-octanol partition coefficients applied to the SAMPL6 logP blind challenge. - Michael R. Jones; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2020)

Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water-octanol partition coefficients in the SAMPL6 challenge. - Andreas Krämer; Phillip S. Hudson; Michael R. Jones; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2020)

SAMPL6 logP challenge: machine learning and quantum mechanical approaches. - Prajay Patel; David M. Kuntz; Michael R. Jones; Bernard R. Brooks; Angela K. Wilson (J. Comput. Aided Mol. Des., 2020)

A deep learning approach for the blind logP prediction in SAMPL6 challenge. - Samarjeet Prasad; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2020)

Variational embedding of protein folding simulations using gaussian mixture variational autoencoders. - Mahdi Ghorbani; Samarjeet Prasad; Jeffery B. Klauda; Bernard R. Brooks (CoRR, 2021)

A replica exchange umbrella sampling (REUS) approach to predict host-guest binding free energies in SAMPL8 challenge. - Mahdi Ghorbani; Phillip S. Hudson; Michael R. Jones; Félix Aviat; Rubén Meana-Pañeda; Jeffery B. Klauda; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2021)

The Extended Eighth-Shell method for periodic boundary conditions with rotational symmetry. - Samarjeet Prasad; Andrew C. Simmonett; Rubén Meana-Pañeda; Bernard R. Brooks (J. Comput. Chem., 2021)

GraphVAMPNet, using graph neural networks and variational approach to markov processes for dynamical modeling of biomolecules. - Mahdi Ghorbani; Samarjeet Prasad; Jeffery B. Klauda; Bernard R. Brooks (CoRR, 2022)

Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches. - 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 (J. Comput. Aided Mol. Des., 2022)

MPI-parallelization of the grid inhomogeneous solvation theory calculation. - Daniel R. Roe; Bernard R. Brooks (J. Comput. Chem., 2024)

Leveraging-Induced Polarization for Drug Discovery: Efficient IC50 Prediction Using Minimal Features. - Ashraf Mohamed; Bernard R. Brooks; Muhamed Amin (J. Chem. Inf. Model., 2025)

Boltzmann Classifier: A Thermodynamic-Inspired Approach to Supervised Learning. - Muhamed Amin; Bernard R. Brooks (CoRR, 2025)