Charles L. Brooks III

Publication Activity (10 Years)

Years Active: 1991-2024
Publications (10 Years): 19

Top Topics

Molecular Dynamics

Graphics Processors

Top Venues

J. Comput. Chem.

J. Chem. Inf. Model.

J. Comput. Aided Mol. Des.

Publications

Arghya Chakravorty, Azam Hussain, Luis F. Cervantes, Thanh T. Lai, Charles L. Brooks III
Exploring the Limits of the Generalized CHARMM and AMBER Force Fields through Predictions of Hydration Free Energy of Small Molecules. J. Chem. Inf. Model. 64 (10) (2024)
Parveen Gartan, Fahimeh Khorsand, Pushpak Mizar, Juha Ilmari Vahokovski, Luis F. Cervantes, Bengt Erik Haug, Ruth Brenk, Charles L. Brooks III, Nathalie Reuter
Investigating Polypharmacology through Targeting Known Human Neutrophil Elastase Inhibitors to Proteinase 3. J. Chem. Inf. Model. 64 (3) (2024)
Furyal Ahmed, Charles L. Brooks III
FASTDock: A Pipeline for Allosteric Drug Discovery. J. Chem. Inf. Model. 63 (22) (2023)
Yujin Wu, Charles L. Brooks III
Covalent docking in CDOCKER. J. Comput. Aided Mol. Des. 36 (8) (2022)
Ellen E. Guest, Luis F. Cervantes, Stephen D. Pickett, Charles L. Brooks III, Jonathan D. Hirst
Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4. J. Chem. Inf. Model. 62 (6) (2022)
Jonah Z. Vilseck, Luis F. Cervantes, Ryan L. Hayes, Charles L. Brooks III
Optimizing Multisite λ-Dynamics Throughput with Charge Renormalization. J. Chem. Inf. Model. 62 (6) (2022)
Amanda L. Peiffer, Julie M. Garlick, Stephen T. Joy, Anna K. Mapp, Charles L. Brooks III
Allostery in the dynamic coactivator domain KIX occurs through minor conformational micro-states. PLoS Comput. Biol. 18 (4) (2022)
Yujin Wu, Charles L. Brooks III
Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy. J. Chem. Inf. Model. 61 (11) (2021)
Ryan L. Hayes, Charles L. Brooks III
A strategy for proline and glycine mutations to proteins with alchemical free energy calculations. J. Comput. Chem. 42 (15) (2021)
Daniel Montiel-Garcia, Nelly Beatriz Santoyo-Rivera, Phuong Ho, Mauricio Carrillo-Tripp, Charles L. Brooks III, John E. Johnson, Vijay S. Reddy
VIPERdb v3.0: a structure-based data analytics platform for viral capsids. Nucleic Acids Res. 49 (Database-Issue) (2021)
Xiping Gong, Mara Chiricotto, Xiaorong Liu, Erik Nordquist, Michael Feig, Charles L. Brooks III, Jianhan Chen
Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units. J. Comput. Chem. 41 (8) (2020)
Xinqiang Ding, Ryan L. Hayes, Jonah Z. Vilseck, Murchtricia K. Charles, Charles L. Brooks III
CDOCKER and λ-dynamics for prospective prediction in D3R Grand Challenge 2. J. Comput. Aided Mol. Des. 32 (1) (2018)
Seonghoon Kim, Jumin Lee, Sunhwan Jo, Charles L. Brooks III, Hui Sun Lee, Wonpil Im
CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules. J. Comput. Chem. 38 (21) (2017)
Shuai Wei, Charles L. Brooks III, Aaron T. Frank
A rapid solvent accessible surface area estimator for coarse grained molecular simulations. J. Comput. Chem. 38 (15) (2017)
Evan J. Arthur, Charles L. Brooks III
Efficient implementation of constant pH molecular dynamics on modern graphics processors. J. Comput. Chem. 37 (24) (2016)
Jessica K. Gagnon, Sean M. Law, Charles L. Brooks III
Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM. J. Comput. Chem. 37 (8) (2016)
Evan J. Arthur, Charles L. Brooks III
Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors. J. Comput. Chem. 37 (10) (2016)
Alex Dickson, Logan S. Ahlstrom, Charles L. Brooks III
Coupled folding and binding with 2D Window-Exchange Umbrella Sampling. J. Comput. Chem. 37 (6) (2016)
Shanshan Cheng, Yang Zhang, Charles L. Brooks III
PCalign: a method to quantify physicochemical similarity of protein-protein interfaces. BMC Bioinform. 16 (2015)
Sean M. Law, Aaron T. Frank, Charles L. Brooks III
PCASSO: A fast and efficient Cα-based method for accurately assigning protein secondary structure elements. J. Comput. Chem. 35 (24) (2014)
Charles L. Brooks III, Masahiro Ehara, Gernot Frenking, Peter R. Schreiner
New paint and a new engine. J. Comput. Chem. 34 (1) (2013)
Alex Dickson, Charles L. Brooks III
. PLoS Comput. Biol. 9 (11) (2013)
Jennifer L. Knight, Joseph D. Yesselman, Charles L. Brooks III
Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes. J. Comput. Chem. 34 (11) (2013)
Shanshan Cheng, Charles L. Brooks III
Viral Capsid Proteins Are Segregated in Structural Fold Space. PLoS Comput. Biol. 9 (2) (2013)
Joseph D. Yesselman, Daniel J. Price, Jennifer L. Knight, Charles L. Brooks III
MATCH: An atom-typing toolset for molecular mechanics force fields. J. Comput. Chem. 33 (2) (2012)
Ranjan V. Mannige, Charles L. Brooks III, Eugene I. Shakhnovich
A Universal Trend among Proteomes Indicates an Oily Last Common Ancestor. PLoS Comput. Biol. 8 (12) (2012)
Jennifer L. Knight, Charles L. Brooks III
Surveying implicit solvent models for estimating small molecule absolute hydration free energies. J. Comput. Chem. 32 (13) (2011)
Jennifer L. Knight, Charles L. Brooks III
Applying efficient implicit nongeometric constraints in alchemical free energy simulations. J. Comput. Chem. 32 (16) (2011)
Obaidur Rahaman, Trilce Estrada, Douglas J. Doren, Michela Taufer, Charles L. Brooks III, Roger S. Armen
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. J. Chem. Inf. Model. 51 (9) (2011)
Jennifer L. Knight, Charles L. Brooks III
lambda-Dynamics free energy simulation methods. J. Comput. Chem. 30 (11) (2009)
Gernot Frenking, Charles L. Brooks III, Shigeyoshi Sakaki
Editors' note. J. Comput. Chem. 30 (1) (2009)
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
: an enhanced and web API enabled relational database for structural virology. Nucleic Acids Res. 37 (Database-Issue) (2009)
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, V. 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
CHARMM: The biomolecular simulation program. J. Comput. Chem. 30 (10) (2009)
Charles L. Brooks III
De novo modeling of GPCR class A structures. IPDPS (2009)
Mark A. Olson, Michael Feig, Charles L. Brooks III
Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions. J. Comput. Chem. 29 (5) (2008)
David L. Bostick, Charles L. Brooks III
Deprotonation by Dehydration: The Origin of Ammonium Sensing in the AmtB Channel. PLoS Comput. Biol. 3 (2) (2007)
Michela Taufer, Andre Kerstens, Trilce Estrada, David A. Flores, Richard Zamudio, Patricia J. Teller, Roger S. Armen, Charles L. Brooks III
Moving Volunteer Computing towards Knowledge-Constructed, Dynamically-Adaptive Modeling and Scheduling. IPDPS (2007)
Charles L. Brooks III, Gernot Frenking, Shigeyoshi Sakaki
Letter from the Editors. J. Comput. Chem. 28 (11) (2007)
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
VIPERdb: a relational database for structural virology. Nucleic Acids Res. 34 (Database-Issue) (2006)
Michela Taufer, Chahm An, Andreas Kerstens, Charles L. Brooks III
Predictor@Home: A "Protein Structure Prediction Supercomputer' Based on Global Computing. IEEE Trans. Parallel Distributed Syst. 17 (8) (2006)
Jianhan Chen, Wonpil Im, Charles L. Brooks III
Application of torsion angle molecular dynamics for efficient sampling of protein conformations. J. Comput. Chem. 26 (15) (2005)
Daniel J. Price, Charles L. Brooks III
Detailed considerations for a balanced and broadly applicable force field: A study of substituted benzenes modeled with OPLS-AA. J. Comput. Chem. 26 (14) (2005)
Michela Taufer, Chahm An, Andreas Kerstens, Charles L. Brooks III
Predictor@Home: A "Protein Structure Prediction Supercomputer" Based on Public-Resource Computing. IPDPS (2005)
Michela Taufer, Patricia J. Teller, David P. Anderson, Charles L. Brooks III
Metrics for Effective Resource Management in Global Computing Environments. e-Science (2005)
Michela Taufer, Michael Crowley, Daniel J. Price, Andrew A. Chien, Charles L. Brooks III
Study of a highly accurate and fast protein-ligand docking method based on molecular dynamics. Concurr. Comput. Pract. Exp. 17 (14) (2005)
Michela Taufer, David P. Anderson, Pietro Cicotti, Charles L. Brooks III
Homogeneous Redundancy: a Technique to Ensure Integrity of Molecular Simulation Results Using Public Computing. IPDPS (2005)
Charles L. Brooks III
Editorial. J. Comput. Chem. 26 (16) (2005)
Michael Feig, Alexey Onufriev, Michael S. Lee, Wonpil Im, David A. Case, Charles L. Brooks III
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. J. Comput. Chem. 25 (2) (2004)
Anand Natrajan, Michael Crowley, Nancy Wilkins-Diehr, Marty A. Humphrey, Anthony D. Fox, Andrew S. Grimshaw, Charles L. Brooks III
Studying protein folding on the Grid: experiences using CHARMM on NPACI resources under Legion. Concurr. Comput. Pract. Exp. 16 (4) (2004)
Sandeep Patel, Charles L. Brooks III
CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations. J. Comput. Chem. 25 (1) (2004)
Sandeep Patel, Alexander D. MacKerell Jr., Charles L. Brooks III
CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. J. Comput. Chem. 25 (12) (2004)
Alexander D. MacKerell Jr., Michael Feig, Charles L. Brooks III
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. J. Comput. Chem. 25 (11) (2004)
Michela Taufer, Michael Crowley, Daniel J. Price, Andrew A. Chien, Charles L. Brooks III
Study of a Highly Accurate and Fast Protein-Ligand Docking Algorithm Based on Molecular Dynamics. IPDPS (2004)
Derrick Kondo, Michela Taufer, Charles L. Brooks III, Henri Casanova, Andrew A. Chien
Characterizing and Evaluating Desktop Grids: An Empirical Study. IPDPS (2004)
Olgun Guvench, Charles L. Brooks III
Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations. J. Comput. Chem. 25 (8) (2004)
Wonpil Im, Michael S. Lee, Charles L. Brooks III
Generalized born model with a simple smoothing function. J. Comput. Chem. 24 (14) (2003)
Guosheng Wu, Daniel H. Robertson, Charles L. Brooks III, Michal Vieth
Detailed analysis of grid-based molecular docking: A case study of CDOCKER - A CHARMm-based MD docking algorithm. J. Comput. Chem. 24 (13) (2003)
Badry D. Bursulaya, Maxim Totrov, Ruben Abagyan, Charles L. Brooks III
Comparative study of several algorithms for flexible ligand docking. J. Comput. Aided Mol. Des. 17 (11) (2003)
Michael S. Lee, Michael Feig, Freddie R. Salsbury Jr., Charles L. Brooks III
New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations. J. Comput. Chem. 24 (11) (2003)
Michael S. Lee, Michael Feig, Freddie R. Salsbury Jr., Charles L. Brooks III
New analytic approximation to the standard molecular volume definition and its application to generalized born calculations - Erratum. J. Comput. Chem. 24 (14) (2003)
Brian N. Dominy, Charles L. Brooks III
Identifying native-like protein structures using physics-based potentials. J. Comput. Chem. 23 (1) (2002)
Daniel J. Price, Charles L. Brooks III
Modern protein force fields behave comparably in molecular dynamics simulations. J. Comput. Chem. 23 (11) (2002)
Anand Natrajan, Anthony D. Fox, Marty A. Humphrey, Andrew S. Grimshaw, Nancy Wilkins-Diehr, Michael Crowley, Charles L. Brooks III
Studying Protein Folding on the Grid: Experiences Using CHARMM on NPACI Resources under Legion. HPDC (2001)
Michal Vieth, Jonathan D. Hirst, Brian N. Dominy, Heidi Daigler, Charles L. Brooks III
Assessing search strategies for flexible docking. J. Comput. Chem. 19 (14) (1998)
Michal Vieth, Jonathan D. Hirst, Andrzej Kolinski, Charles L. Brooks III
Assessing energy functions for flexible docking. J. Comput. Chem. 19 (14) (1998)
William S. Young, Charles L. Brooks III
Dynamic Load Balancing Algorithms for Replicated Data Molecular Dynamics. J. Comput. Chem. 16 (6) (1995)
William S. Young, Charles L. Brooks III
Implementation of a Data Parallel, Logical Domain Decomposition Method for Interparticle Interactions in Molecular Dynamics of Structured Molecular Fluids. J. Comput. Chem. 15 (1) (1994)
Charles L. Brooks III, William S. Young, Douglas J. Tobias
Molecular Simulations On Supercomputers. Int. J. High Perform. Comput. Appl. 5 (4) (1991)