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ORCIDCharles L. Brooks III
Person information
- affiliation: University of Michigan, Department of Chemistry, Ann Arbor, USA
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2020 – today
- 2024
[j60]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): 621-626 (2024)- [j59]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): 4089-4101 (2024) - 2023
- [j58]Furyal Ahmed, Charles L. Brooks III:
FASTDock: A Pipeline for Allosteric Drug Discovery. J. Chem. Inf. Model. 63(22): 7219-7227 (2023) - 2022
- [j57]Yujin Wu, Charles L. Brooks III:
Covalent docking in CDOCKER. J. Comput. Aided Mol. Des. 36(8): 563-574 (2022) - [j56]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): 1458-1470 (2022) - [j55]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): 1479-1488 (2022) - [j54]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) - 2021
- [j53]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): 1088-1094 (2021) - [j52]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): 5535-5549 (2021) - [j51]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): D809-D816 (2021) - 2020
- [j50]Xiping Gong, Mara Chiricotto, Xiaorong Liu, Erik B. 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): 830-838 (2020)
2010 – 2019
- 2018
- [j49]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): 89-102 (2018) - 2017
- [j48]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): 1270-1274 (2017) - [j47]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): 1879-1886 (2017) - 2016
- [j46]Alex Dickson, Logan S. Ahlstrom, Charles L. Brooks III:
Coupled folding and binding with 2D Window-Exchange Umbrella Sampling. J. Comput. Chem. 37(6): 587-594 (2016) - [j45]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): 753-762 (2016) - [j44]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): 927-939 (2016) - [j43]Evan J. Arthur, Charles L. Brooks III:
Efficient implementation of constant pH molecular dynamics on modern graphics processors. J. Comput. Chem. 37(24): 2171-2180 (2016) - 2015
- [j42]Shanshan Cheng, Yang Zhang, Charles L. Brooks III:
PCalign: a method to quantify physicochemical similarity of protein-protein interfaces. BMC Bioinform. 16: 33:1-33:12 (2015) - 2014
- [j41]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): 1757-1761 (2014) - 2013
- [j40]Charles L. Brooks III, Masahiro Ehara, Gernot Frenking, Peter R. Schreiner:
New paint and a new engine. J. Comput. Chem. 34(1): 1 (2013) - [j39]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): 893-903 (2013) - [j38]Shanshan Cheng, Charles L. Brooks III:
Viral Capsid Proteins Are Segregated in Structural Fold Space. PLoS Comput. Biol. 9(2) (2013) - [j37]Alex Dickson, Charles L. Brooks III:
Quantifying Chaperone-Mediated Transitions in the Proteostasis Network of E. coli. PLoS Comput. Biol. 9(11) (2013) - 2012
- [j36]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): 189-202 (2012) - [j35]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) - 2011
- [j34]Jennifer L. Knight, Charles L. Brooks III:
Surveying implicit solvent models for estimating small molecule absolute hydration free energies. J. Comput. Chem. 32(13): 2909-2923 (2011) - [j33]Jennifer L. Knight, Charles L. Brooks III:
Applying efficient implicit nongeometric constraints in alchemical free energy simulations. J. Comput. Chem. 32(16): 3423-3432 (2011) - [j32]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): 2047-2065 (2011)
2000 – 2009
- 2009
- [j31]Gernot Frenking, Charles L. Brooks III, Shigeyoshi Sakaki:
Editors' note. J. Comput. Chem. 30(1): 1 (2009) - [j30]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:
CHARMM: The biomolecular simulation program. J. Comput. Chem. 30(10): 1545-1614 (2009) - [j29]Jennifer L. Knight, Charles L. Brooks III:
lambda-Dynamics free energy simulation methods. J. Comput. Chem. 30(11): 1692-1700 (2009) - [j28]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:
VIPERdb2: an enhanced and web API enabled relational database for structural virology. Nucleic Acids Res. 37(Database-Issue): 436-442 (2009) - [c8]Charles L. Brooks III:
De novo modeling of GPCR class A structures. IPDPS 2009: 1 - 2008
- [j27]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): 820-831 (2008) - 2007
- [j26]Charles L. Brooks III, Gernot Frenking, Shigeyoshi Sakaki:
Letter from the Editors. J. Comput. Chem. 28(11): 1775 (2007) - [j25]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) - [c7]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: 1-8 - 2006
- [j24]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): 386-389 (2006) - [j23]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): 786-796 (2006) - 2005
- [j22]Michela Taufer, Michael F. 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): 1627-1641 (2005) - [j21]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): 1529-1541 (2005) - [j20]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): 1565-1578 (2005) - [j19]Charles L. Brooks III:
Editorial. J. Comput. Chem. 26(16): 1667 (2005) - [c6]Michela Taufer, Patricia J. Teller, David P. Anderson, Charles L. Brooks III:
Metrics for Effective Resource Management in Global Computing Environments. e-Science 2005: 204-211 - [c5]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 - [c4]Michela Taufer, Chahm An, Andreas Kerstens, Charles L. Brooks III:
Predictor@Home: A "Protein Structure Prediction Supercomputer" Based on Public-Resource Computing. IPDPS 2005 - 2004
- [j18]Anand Natrajan, Michael F. 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): 385-397 (2004) - [j17]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): 1-16 (2004) - [j16]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): 265-284 (2004) - [j15]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): 1005-1014 (2004) - [j14]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): 1400-1415 (2004) - [j13]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): 1504-1514 (2004) - [c3]Derrick Kondo, Michela Taufer, Charles L. Brooks III, Henri Casanova, Andrew A. Chien:
Characterizing and Evaluating Desktop Grids: An Empirical Study. IPDPS 2004 - [c2]Michela Taufer, Michael F. 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 - 2003
- [j12]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): 755-763 (2003) - [j11]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): 1348-1356 (2003) - [j10]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): 1549-1562 (2003) - [j9]Wonpil Im, Michael S. Lee, Charles L. Brooks III:
Generalized born model with a simple smoothing function. J. Comput. Chem. 24(14): 1691-1702 (2003) - [j8]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): 1821 (2003) - 2002
- [j7]Brian N. Dominy, Charles L. Brooks III:
Identifying native-like protein structures using physics-based potentials. J. Comput. Chem. 23(1): 147-160 (2002) - [j6]Daniel J. Price, Charles L. Brooks III:
Modern protein force fields behave comparably in molecular dynamics simulations. J. Comput. Chem. 23(11): 1045-1057 (2002) - 2001
- [c1]Anand Natrajan, Anthony D. Fox, Marty A. Humphrey, Andrew S. Grimshaw, Nancy Wilkins-Diehr, Michael F. Crowley, Charles L. Brooks III:
Studying Protein Folding on the Grid: Experiences Using CHARMM on NPACI Resources under Legion. HPDC 2001: 14-21
1990 – 1999
- 1998
- [j5]Michal Vieth, Jonathan D. Hirst, Andrzej Kolinski, Charles L. Brooks III:
Assessing energy functions for flexible docking. J. Comput. Chem. 19(14): 1612-1622 (1998) - [j4]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): 1623-1631 (1998) - 1995
- [j3]William S. Young, Charles L. Brooks III:
Dynamic Load Balancing Algorithms for Replicated Data Molecular Dynamics. J. Comput. Chem. 16(6): 715-722 (1995) - 1994
- [j2]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): 44-53 (1994) - 1991
- [j1]Charles L. Brooks III, William S. Young, Douglas J. Tobias:
Molecular Simulations On Supercomputers. Int. J. High Perform. Comput. Appl. 5(4): 98-112 (1991)
Coauthor Index
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