Molecular Simulations On Supercomputers. - Charles L. Brooks III; William S. Young; Douglas J. Tobias (Int. J. High Perform. Comput. Appl., 1991)

Implementation of a Data Parallel, Logical Domain Decomposition Method for Interparticle Interactions in Molecular Dynamics of Structured Molecular Fluids. - William S. Young; Charles L. Brooks III (J. Comput. Chem., 1994)

Dynamic Load Balancing Algorithms for Replicated Data Molecular Dynamics. - William S. Young; Charles L. Brooks III (J. Comput. Chem., 1995)

Assessing search strategies for flexible docking. - Michal Vieth; Jonathan D. Hirst; Brian N. Dominy; Heidi Daigler; Charles L. Brooks III (J. Comput. Chem., 1998)

Assessing energy functions for flexible docking. - Michal Vieth; Jonathan D. Hirst; Andrzej Kolinski; Charles L. Brooks III (J. Comput. Chem., 1998)

Identifying native-like protein structures using physics-based potentials. - Brian N. Dominy; Charles L. Brooks III (J. Comput. Chem., 2002)

Modern protein force fields behave comparably in molecular dynamics simulations. - Daniel J. Price; Charles L. Brooks III (J. Comput. Chem., 2002)

Comparative study of several algorithms for flexible ligand docking. - Badry D. Bursulaya; Maxim Totrov; Ruben Abagyan; Charles L. Brooks III (J. Comput. Aided Mol. Des., 2003)

Generalized born model with a simple smoothing function. - Wonpil Im; Michael S. Lee; Charles L. Brooks III (J. Comput. Chem., 2003)

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations. - Michael S. Lee; Michael Feig; Freddie R. Salsbury Jr.; Charles L. Brooks III (J. Comput. Chem., 2003)

New analytic approximation to the standard molecular volume definition and its application to generalized born calculations - Erratum. - Michael S. Lee; Michael Feig; Freddie R. Salsbury Jr.; Charles L. Brooks III (J. Comput. Chem., 2003)

Detailed analysis of grid-based molecular docking: A case study of CDOCKER - A CHARMm-based MD docking algorithm. - Guosheng Wu; Daniel H. Robertson; Charles L. Brooks III; Michal Vieth (J. Comput. Chem., 2003)

Characterizing and Evaluating Desktop Grids: An Empirical Study. - Derrick Kondo; Michela Taufer; Charles L. Brooks III; Henri Casanova; Andrew A. Chien (IPDPS, 2004)

Study of a Highly Accurate and Fast Protein-Ligand Docking Algorithm Based on Molecular Dynamics. - Michela Taufer; Michael F. Crowley; Daniel J. Price; Andrew A. Chien; Charles L. Brooks III (IPDPS, 2004)

Studying protein folding on the Grid: experiences using CHARMM on NPACI resources under Legion. - Anand Natrajan; Michael F. Crowley; Nancy Wilkins-Diehr; Marty A. Humphrey; Anthony D. Fox; Andrew S. Grimshaw; Charles L. Brooks III (Concurr. Comput. Pract. Exp., 2004)

Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. - Michael Feig; Alexey Onufriev; Michael S. Lee; Wonpil Im; David A. Case; Charles L. Brooks III (J. Comput. Chem., 2004)

Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations. - Olgun Guvench; Charles L. Brooks III (J. Comput. Chem., 2004)

Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. - Alexander D. MacKerell Jr.; Michael Feig; Charles L. Brooks III (J. Comput. Chem., 2004)

CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations. - Sandeep Patel; Charles L. Brooks III (J. Comput. Chem., 2004)

CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. - Sandeep Patel; Alexander D. MacKerell Jr.; Charles L. Brooks III (J. Comput. Chem., 2004)

Metrics for Effective Resource Management in Global Computing Environments. - Michela Taufer; Patricia J. Teller; David P. Anderson; Charles L. Brooks III (e-Science, 2005)

Homogeneous Redundancy: a Technique to Ensure Integrity of Molecular Simulation Results Using Public Computing. - Michela Taufer; David P. Anderson; Pietro Cicotti; Charles L. Brooks III (IPDPS, 2005)

Predictor@Home: A "Protein Structure Prediction Supercomputer" Based on Public-Resource Computing. - Michela Taufer; Chahm An; Andreas Kerstens; Charles L. Brooks III (IPDPS, 2005)

Study of a highly accurate and fast protein-ligand docking method based on molecular dynamics. - Michela Taufer; Michael F. Crowley; Daniel J. Price; Andrew A. Chien; Charles L. Brooks III (Concurr. Comput. Pract. Exp., 2005)

Editorial. - Charles L. Brooks III (J. Comput. Chem., 2005)

Application of torsion angle molecular dynamics for efficient sampling of protein conformations. - Jianhan Chen; Wonpil Im; Charles L. Brooks III (J. Comput. Chem., 2005)

Detailed considerations for a balanced and broadly applicable force field: A study of substituted benzenes modeled with OPLS-AA. - Daniel J. Price; Charles L. Brooks III (J. Comput. Chem., 2005)

VIPERdb: a relational database for structural virology. - Craig M. Shepherd; Ian A. Borelli; Gabriel Lander; Padmaja Natarajan; Vinay Siddavanahalli; Chandrajit L. Bajaj; John E. Johnson; Charles L. Brooks III; Vijay S. Reddy (Nucleic Acids Res., 2006)

Predictor@Home: A "Protein Structure Prediction Supercomputer' Based on Global Computing. - Michela Taufer; Chahm An; Andreas Kerstens; Charles L. Brooks III (IEEE Trans. Parallel Distributed Syst., 2006)

Moving Volunteer Computing towards Knowledge-Constructed, Dynamically-Adaptive Modeling and Scheduling. - Michela Taufer; Andre Kerstens; Trilce Estrada; David A. Flores; Richard Zamudio; Patricia J. Teller; Roger S. Armen; Charles L. Brooks III (IPDPS, 2007)

Letter from the Editors. - Charles L. Brooks III; Gernot Frenking; Shigeyoshi Sakaki (J. Comput. Chem., 2007)

Deprotonation by Dehydration: The Origin of Ammonium Sensing in the AmtB Channel. - David L. Bostick; Charles L. Brooks III (PLoS Comput. Biol., 2007)

Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions. - Mark A. Olson; Michael Feig; Charles L. Brooks III (J. Comput. Chem., 2008)

De novo modeling of GPCR class A structures. - Charles L. Brooks III (IPDPS, 2009)

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)

Editors' note. - Gernot Frenking; Charles L. Brooks III; Shigeyoshi Sakaki (J. Comput. Chem., 2009)

lambda-Dynamics free energy simulation methods. - Jennifer L. Knight; Charles L. Brooks III (J. Comput. Chem., 2009)

VIPERdb2: an enhanced and web API enabled relational database for structural virology. - Mauricio Carrillo-Tripp; Craig M. Shepherd; Ian A. Borelli; Sangita Venkataraman; Gabriel Lander; Padmaja Natarajan; John E. Johnson; Charles L. Brooks III; Vijay S. Reddy (Nucleic Acids Res., 2009)

Surveying implicit solvent models for estimating small molecule absolute hydration free energies. - Jennifer L. Knight; Charles L. Brooks III (J. Comput. Chem., 2011)

Applying efficient implicit nongeometric constraints in alchemical free energy simulations. - Jennifer L. Knight; Charles L. Brooks III (J. Comput. Chem., 2011)

Evaluation of Several Two-Step Scoring Functions Based on Linear Interaction Energy, Effective Ligand Size, and Empirical Pair Potentials for Prediction of Protein-Ligand Binding Geometry and Free Energy. - Obaidur Rahaman; Trilce Estrada; Douglas J. Doren; Michela Taufer; Charles L. Brooks III; Roger S. Armen (J. Chem. Inf. Model., 2011)

MATCH: An atom-typing toolset for molecular mechanics force fields. - Joseph D. Yesselman; Daniel J. Price; Jennifer L. Knight; Charles L. Brooks III (J. Comput. Chem., 2012)

A Universal Trend among Proteomes Indicates an Oily Last Common Ancestor. - Ranjan V. Mannige; Charles L. Brooks III; Eugene I. Shakhnovich (PLoS Comput. Biol., 2012)

New paint and a new engine. - Charles L. Brooks III; Masahiro Ehara; Gernot Frenking; Peter R. Schreiner (J. Comput. Chem., 2013)

Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes. - Jennifer L. Knight; Joseph D. Yesselman; Charles L. Brooks III (J. Comput. Chem., 2013)

Viral Capsid Proteins Are Segregated in Structural Fold Space. - Shanshan Cheng; Charles L. Brooks III (PLoS Comput. Biol., 2013)

Quantifying Chaperone-Mediated Transitions in the Proteostasis Network of E. coli. - Alex Dickson; Charles L. Brooks III (PLoS Comput. Biol., 2013)

PCASSO: A fast and efficient Cα-based method for accurately assigning protein secondary structure elements. - Sean M. Law; Aaron T. Frank; Charles L. Brooks III (J. Comput. Chem., 2014)

PCalign: a method to quantify physicochemical similarity of protein-protein interfaces. - Shanshan Cheng; Yang Zhang 040; Charles L. Brooks III (BMC Bioinform., 2015)

Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors. - Evan J. Arthur; Charles L. Brooks III (J. Comput. Chem., 2016)

Efficient implementation of constant pH molecular dynamics on modern graphics processors. - Evan J. Arthur; Charles L. Brooks III (J. Comput. Chem., 2016)

Coupled folding and binding with 2D Window-Exchange Umbrella Sampling. - Alex Dickson; Logan S. Ahlstrom; Charles L. Brooks III (J. Comput. Chem., 2016)

Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM. - Jessica K. Gagnon; Sean M. Law; Charles L. Brooks III (J. Comput. Chem., 2016)

CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules. - Seonghoon Kim; Jumin Lee; Sunhwan Jo; Charles L. Brooks III; Hui Sun Lee; Wonpil Im (J. Comput. Chem., 2017)

A rapid solvent accessible surface area estimator for coarse grained molecular simulations. - Shuai Wei; Charles L. Brooks III; Aaron T. Frank (J. Comput. Chem., 2017)

CDOCKER and λ-dynamics for prospective prediction in D3R Grand Challenge 2. - Xinqiang Ding; Ryan L. Hayes; Jonah Z. Vilseck; Murchtricia K. Charles; Charles L. Brooks III (J. Comput. Aided Mol. Des., 2018)

Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units. - Xiping Gong; Mara Chiricotto; Xiaorong Liu; Erik B. Nordquist; Michael Feig; Charles L. Brooks III; Jianhan Chen (J. Comput. Chem., 2020)

A strategy for proline and glycine mutations to proteins with alchemical free energy calculations. - Ryan L. Hayes; Charles L. Brooks III (J. Comput. Chem., 2021)

Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy. - Yujin Wu; Charles L. Brooks III (J. Chem. Inf. Model., 2021)

VIPERdb v3.0: a structure-based data analytics platform for viral capsids. - Daniel Montiel-Garcia; Nelly Beatriz Santoyo-Rivera; Phuong Ho; Mauricio Carrillo-Tripp; Charles L. Brooks III; John E. Johnson; Vijay S. Reddy (Nucleic Acids Res., 2021)

Covalent docking in CDOCKER. - Yujin Wu; Charles L. Brooks III (J. Comput. Aided Mol. Des., 2022)

Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4. - Ellen E. Guest; Luis F. Cervantes; Stephen D. Pickett; Charles L. Brooks III; Jonathan D. Hirst (J. Chem. Inf. Model., 2022)

Optimizing Multisite λ-Dynamics Throughput with Charge Renormalization. - Jonah Z. Vilseck; Luis F. Cervantes; Ryan L. Hayes; Charles L. Brooks III (J. Chem. Inf. Model., 2022)

Allostery in the dynamic coactivator domain KIX occurs through minor conformational micro-states. - Amanda L. Peiffer; Julie M. Garlick; Stephen T. Joy; Anna K. Mapp; Charles L. Brooks III (PLoS Comput. Biol., 2022)

FASTDock: A Pipeline for Allosteric Drug Discovery. - Furyal Ahmed; Charles L. Brooks III (J. Chem. Inf. Model., 2023)

Exploring the Limits of the Generalized CHARMM and AMBER Force Fields through Predictions of Hydration Free Energy of Small Molecules. - Arghya Chakravorty; Azam Hussain; Luis F. Cervantes; Thanh T. Lai; Charles L. Brooks III (J. Chem. Inf. Model., 2024)

Investigating Polypharmacology through Targeting Known Human Neutrophil Elastase Inhibitors to Proteinase 3. - Parveen Gartan; Fahimeh Khorsand; Pushpak Mizar; Juha Ilmari Vahokovski; Luis F. Cervantes; Bengt Erik Haug; Ruth Brenk; Charles L. Brooks III; Nathalie Reuter (J. Chem. Inf. Model., 2024)

Core Flipping in Lead Optimization: Rank Ordering Using λ-Dynamics. - Parveen Gartan; Charles L. Brooks III; Nathalie Reuter (J. Chem. Inf. Model., 2025)