Charles L. Brooks III

70 papers A 7B 1Journal 62

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Core Flipping in Lead Optimization: Rank Ordering Using λ-Dynamics. J. Chem. Inf. Model. Parveen Gartan, Charles L. Brooks III, Nathalie Reuter
2024	J	`jnl`	Exploring the Limits of the Generalized CHARMM and AMBER Force Fields through Predictions of Hydration Free Energy of Small Molecules. J. Chem. Inf. Model. Arghya Chakravorty, Azam Hussain, Luis F. Cervantes, Thanh T. Lai, Charles L. Brooks III
2024	J	`jnl`	Guiding discovery of protein sequence-structure-function modeling. Bioinform. Azam Hussain, Charles L. Brooks III
2024	J	`jnl`	Investigating Polypharmacology through Targeting Known Human Neutrophil Elastase Inhibitors to Proteinase 3. J. Chem. Inf. Model. Parveen Gartan, Fahimeh Khorsand, Pushpak Mizar, Juha Ilmari Vahokovski, Luis F. Cervantes, Bengt Erik Haug, Ruth Brenk, Charles L. Brooks III, Nathalie Reuter
2023	J	`jnl`	FASTDock: A Pipeline for Allosteric Drug Discovery. J. Chem. Inf. Model. Furyal Ahmed, Charles L. Brooks III
2022	J	`jnl`	Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4. J. Chem. Inf. Model. Ellen E. Guest, Luis F. Cervantes, Stephen D. Pickett, Charles L. Brooks III, Jonathan D. Hirst
2022	J	`jnl`	Allostery in the dynamic coactivator domain KIX occurs through minor conformational micro-states. PLoS Comput. Biol. Amanda L. Peiffer, Julie M. Garlick, Stephen T. Joy, Anna K. Mapp, Charles L. Brooks III
2022	J	`jnl`	Covalent docking in CDOCKER. J. Comput. Aided Mol. Des. Yujin Wu, Charles L. Brooks III
2022	J	`jnl`	Optimizing Multisite λ-Dynamics Throughput with Charge Renormalization. J. Chem. Inf. Model. Jonah Z. Vilseck, Luis F. Cervantes, Ryan L. Hayes, Charles L. Brooks III
2021	J	`jnl`	A strategy for proline and glycine mutations to proteins with alchemical free energy calculations. J. Comput. Chem. Ryan L. Hayes, Charles L. Brooks III
2021	J	`jnl`	Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy. J. Chem. Inf. Model. Yujin Wu, Charles L. Brooks III
2021	J	`jnl`	VIPERdb v3.0: a structure-based data analytics platform for viral capsids. Nucleic Acids Res. Daniel Montiel-Garcia, Nelly Beatriz Santoyo-Rivera, Phuong Ho, Mauricio Carrillo-Tripp, Charles L. Brooks III, John E. Johnson, Vijay S. Reddy
2020	J	`jnl`	Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units. J. Comput. Chem. Xiping Gong, Mara Chiricotto, Xiaorong Liu, Erik B. Nordquist, Michael Feig, Charles L. Brooks III, Jianhan Chen
2018	J	`jnl`	CDOCKER and λ-dynamics for prospective prediction in D3R Grand Challenge 2. J. Comput. Aided Mol. Des. Xinqiang Ding, Ryan L. Hayes, Jonah Z. Vilseck, Murchtricia K. Charles, Charles L. Brooks III
2017	J	`jnl`	A rapid solvent accessible surface area estimator for coarse grained molecular simulations. J. Comput. Chem. Shuai Wei, Charles L. Brooks III, Aaron T. Frank
2017	J	`jnl`	CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules. J. Comput. Chem. Seonghoon Kim, Jumin Lee, Sunhwan Jo, Charles L. Brooks III, Hui Sun Lee, Wonpil Im
2016	J	`jnl`	Coupled folding and binding with 2D Window-Exchange Umbrella Sampling. J. Comput. Chem. Alex Dickson, Logan S. Ahlstrom, Charles L. Brooks III
2016	J	`jnl`	Efficient implementation of constant pH molecular dynamics on modern graphics processors. J. Comput. Chem. Evan J. Arthur, Charles L. Brooks III
2016	J	`jnl`	Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM. J. Comput. Chem. Jessica K. Gagnon, Sean M. Law, Charles L. Brooks III
2016	J	`jnl`	Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors. J. Comput. Chem. Evan J. Arthur, Charles L. Brooks III
2015	J	`jnl`	PCalign: a method to quantify physicochemical similarity of protein-protein interfaces. BMC Bioinform. Shanshan Cheng, Yang Zhang, Charles L. Brooks III
2014	J	`jnl`	PCASSO: A fast and efficient Cα-based method for accurately assigning protein secondary structure elements. J. Comput. Chem. Sean M. Law, Aaron T. Frank, Charles L. Brooks III
2013	J	`jnl`	Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes. J. Comput. Chem. Jennifer L. Knight, Joseph D. Yesselman, Charles L. Brooks III
2013	J	`jnl`	New paint and a new engine. J. Comput. Chem. Charles L. Brooks III, Masahiro Ehara, Gernot Frenking, Peter R. Schreiner
2013	J	`jnl`	Quantifying Chaperone-Mediated Transitions in the Proteostasis Network of PLoS Comput. Biol. Alex Dickson, Charles L. Brooks III
2013	J	`jnl`	Viral Capsid Proteins Are Segregated in Structural Fold Space. PLoS Comput. Biol. Shanshan Cheng, Charles L. Brooks III
2012	J	`jnl`	A Universal Trend among Proteomes Indicates an Oily Last Common Ancestor. PLoS Comput. Biol. Ranjan V. Mannige, Charles L. Brooks III, Eugene I. Shakhnovich
2012	J	`jnl`	MATCH: An atom-typing toolset for molecular mechanics force fields. J. Comput. Chem. Joseph D. Yesselman, Daniel J. Price, Jennifer L. Knight, Charles L. Brooks III
2011	J	`jnl`	Applying efficient implicit nongeometric constraints in alchemical free energy simulations. J. Comput. Chem. Jennifer L. Knight, Charles L. Brooks III
2011	J	`jnl`	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. Obaidur Rahaman, Trilce Estrada, Douglas J. Doren, Michela Taufer, Charles L. Brooks III, Roger S. Armen
2011	J	`jnl`	Surveying implicit solvent models for estimating small molecule absolute hydration free energies. J. Comput. Chem. Jennifer L. Knight, Charles L. Brooks III
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
2009	A	`conf`	De novo modeling of GPCR class A structures. IPDPS Charles L. Brooks III
2009	J	`jnl`	Editors' note. J. Comput. Chem. Gernot Frenking, Charles L. Brooks III, Shigeyoshi Sakaki
2009	J	`jnl`	VIPERdb Nucleic Acids Res. 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
2009	J	`jnl`	lambda-Dynamics free energy simulation methods. J. Comput. Chem. Jennifer L. Knight, Charles L. Brooks III
2008	J	`jnl`	Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions. J. Comput. Chem. Mark A. Olson, Michael Feig, Charles L. Brooks III
2007	J	`jnl`	Deprotonation by Dehydration: The Origin of Ammonium Sensing in the AmtB Channel. PLoS Comput. Biol. David L. Bostick, Charles L. Brooks III
2007	J	`jnl`	Letter from the Editors. J. Comput. Chem. Charles L. Brooks III, Gernot Frenking, Shigeyoshi Sakaki
2007	A	`conf`	Moving Volunteer Computing towards Knowledge-Constructed, Dynamically-Adaptive Modeling and Scheduling. IPDPS Michela Taufer, Andre Kerstens, Trilce Estrada, David A. Flores, Richard Zamudio, Patricia J. Teller, Roger S. Armen, Charles L. Brooks III
2006	J	`jnl`	Predictor@Home: A "Protein Structure Prediction Supercomputer' Based on Global Computing. IEEE Trans. Parallel Distributed Syst. Michela Taufer, Chahm An, Andreas Kerstens, Charles L. Brooks III
2006	J	`jnl`	VIPERdb: a relational database for structural virology. Nucleic Acids Res. 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
2005	J	`jnl`	Application of torsion angle molecular dynamics for efficient sampling of protein conformations. J. Comput. Chem. Jianhan Chen, Wonpil Im, Charles L. Brooks III
2005	J	`jnl`	Detailed considerations for a balanced and broadly applicable force field: A study of substituted benzenes modeled with OPLS-AA. J. Comput. Chem. Daniel J. Price, Charles L. Brooks III
2005	J	`jnl`	Editorial. J. Comput. Chem. Charles L. Brooks III
2005	A	`conf`	Homogeneous Redundancy: a Technique to Ensure Integrity of Molecular Simulation Results Using Public Computing. IPDPS Michela Taufer, David P. Anderson, Pietro Cicotti, Charles L. Brooks III
2005	B	`conf`	Metrics for Effective Resource Management in Global Computing Environments. e-Science Michela Taufer, Patricia J. Teller, David P. Anderson, Charles L. Brooks III
2005	A	`conf`	Predictor@Home: A "Protein Structure Prediction Supercomputer" Based on Public-Resource Computing. IPDPS Michela Taufer, Chahm An, Andreas Kerstens, Charles L. Brooks III
2005	J	`jnl`	Study of a highly accurate and fast protein-ligand docking method based on molecular dynamics. Concurr. Comput. Pract. Exp. Michela Taufer, Michael F. Crowley, Daniel J. Price, Andrew A. Chien, Charles L. Brooks III
2004	J	`jnl`	CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations. J. Comput. Chem. Sandeep Patel, Charles L. Brooks III
2004	J	`jnl`	CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. J. Comput. Chem. Sandeep Patel, Alexander D. MacKerell Jr., Charles L. Brooks III
2004	A	`conf`	Characterizing and Evaluating Desktop Grids: An Empirical Study. IPDPS Derrick Kondo, Michela Taufer, Charles L. Brooks III, Henri Casanova, Andrew A. Chien
2004	J	`jnl`	Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations. J. Comput. Chem. Olgun Guvench, Charles L. Brooks III
2004	J	`jnl`	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. Alexander D. MacKerell Jr., Michael Feig, Charles L. Brooks III
2004	J	`jnl`	Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. J. Comput. Chem. Michael Feig, Alexey Onufriev, Michael S. Lee, Wonpil Im, David A. Case, Charles L. Brooks III
2004	A	`conf`	Study of a Highly Accurate and Fast Protein-Ligand Docking Algorithm Based on Molecular Dynamics. IPDPS Michela Taufer, Michael F. Crowley, Daniel J. Price, Andrew A. Chien, Charles L. Brooks III
2004	J	`jnl`	Studying protein folding on the Grid: experiences using CHARMM on NPACI resources under Legion. Concurr. Comput. Pract. Exp. Anand Natrajan, Michael F. Crowley, Nancy Wilkins-Diehr, Marty A. Humphrey, Anthony D. Fox, Andrew S. Grimshaw, Charles L. Brooks III
2003	J	`jnl`	Comparative study of several algorithms for flexible ligand docking. J. Comput. Aided Mol. Des. Badry D. Bursulaya, Maxim Totrov, Ruben Abagyan, Charles L. Brooks III
2003	J	`jnl`	Detailed analysis of grid-based molecular docking: A case study of CDOCKER - A CHARMm-based MD docking algorithm. J. Comput. Chem. Guosheng Wu, Daniel H. Robertson, Charles L. Brooks III, Michal Vieth
2003	J	`jnl`	Generalized born model with a simple smoothing function. J. Comput. Chem. Wonpil Im, Michael S. Lee, Charles L. Brooks III
2003	J	`jnl`	New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations. J. Comput. Chem. Michael S. Lee, Michael Feig, Freddie R. Salsbury Jr., Charles L. Brooks III
2003	J	`jnl`	New analytic approximation to the standard molecular volume definition and its application to generalized born calculations - Erratum. J. Comput. Chem. Michael S. Lee, Michael Feig, Freddie R. Salsbury Jr., Charles L. Brooks III
2002	J	`jnl`	Identifying native-like protein structures using physics-based potentials. J. Comput. Chem. Brian N. Dominy, Charles L. Brooks III
2002	J	`jnl`	Modern protein force fields behave comparably in molecular dynamics simulations. J. Comput. Chem. Daniel J. Price, Charles L. Brooks III
2001	A	`conf`	Studying Protein Folding on the Grid: Experiences Using CHARMM on NPACI Resources under Legion. HPDC Anand Natrajan, Anthony D. Fox, Marty A. Humphrey, Andrew S. Grimshaw, Nancy Wilkins-Diehr, Michael F. Crowley, Charles L. Brooks III
1998	J	`jnl`	Assessing energy functions for flexible docking. J. Comput. Chem. Michal Vieth, Jonathan D. Hirst, Andrzej Kolinski, Charles L. Brooks III
1998	J	`jnl`	Assessing search strategies for flexible docking. J. Comput. Chem. Michal Vieth, Jonathan D. Hirst, Brian N. Dominy, Heidi Daigler, Charles L. Brooks III
1995	J	`jnl`	Dynamic Load Balancing Algorithms for Replicated Data Molecular Dynamics. J. Comput. Chem. William S. Young, Charles L. Brooks III
1994	J	`jnl`	Implementation of a Data Parallel, Logical Domain Decomposition Method for Interparticle Interactions in Molecular Dynamics of Structured Molecular Fluids. J. Comput. Chem. William S. Young, Charles L. Brooks III
1991	J	`jnl`	Molecular Simulations On Supercomputers. Int. J. High Perform. Comput. Appl. Charles L. Brooks III, William S. Young, Douglas J. Tobias