Charles L. Brooks III
Orcid: 0000-0002-8149-5417Affiliations:
- University of Michigan, Department of Chemistry, Ann Arbor, USA
According to our database1,
Charles L. Brooks III
authored at least 66 papers
between 1991 and 2024.
Collaborative distances:
Collaborative distances:
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on orcid.org
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Bibliography
2024
Investigating Polypharmacology through Targeting Known Human Neutrophil Elastase Inhibitors to Proteinase 3.
J. Chem. Inf. Model., 2024
2023
J. Chem. Inf. Model., November, 2023
2022
Allostery in the dynamic coactivator domain KIX occurs through minor conformational micro-states.
PLoS Comput. Biol., 2022
J. Chem. Inf. Model., 2022
Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4.
J. Chem. Inf. Model., 2022
2021
Nucleic Acids Res., 2021
Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy.
J. Chem. Inf. Model., 2021
A strategy for proline and glycine mutations to proteins with alchemical free energy calculations.
J. Comput. Chem., 2021
2020
Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units.
J. Comput. Chem., 2020
2018
J. Comput. Aided Mol. Des., 2018
2017
A rapid solvent accessible surface area estimator for coarse grained molecular simulations.
J. Comput. Chem., 2017
CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules.
J. Comput. Chem., 2017
2016
Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM.
J. Comput. Chem., 2016
J. Comput. Chem., 2016
Efficient implementation of constant pH molecular dynamics on modern graphics processors.
J. Comput. Chem., 2016
Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors.
J. Comput. Chem., 2016
2015
PCalign: a method to quantify physicochemical similarity of protein-protein interfaces.
BMC Bioinform., 2015
2014
PCASSO: A fast and efficient Cα-based method for accurately assigning protein secondary structure elements.
J. Comput. Chem., 2014
2013
Quantifying Chaperone-Mediated Transitions in the Proteostasis Network of <i>E. coli</i>.
PLoS Comput. Biol., 2013
PLoS Comput. Biol., 2013
Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes.
J. Comput. Chem., 2013
2012
PLoS Comput. Biol., 2012
J. Comput. Chem., 2012
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.
J. Chem. Inf. Model., 2011
Applying efficient implicit nongeometric constraints in alchemical free energy simulations.
J. Comput. Chem., 2011
Surveying implicit solvent models for estimating small molecule absolute hydration free energies.
J. Comput. Chem., 2011
2009
VIPERdb<sup>2</sup>: an enhanced and web API enabled relational database for structural virology.
Nucleic Acids Res., 2009
Proceedings of the 23rd IEEE International Symposium on Parallel and Distributed Processing, 2009
2008
Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions.
J. Comput. Chem., 2008
2007
PLoS Comput. Biol., 2007
Moving Volunteer Computing towards Knowledge-Constructed, Dynamically-Adaptive Modeling and Scheduling.
Proceedings of the 21th International Parallel and Distributed Processing Symposium (IPDPS 2007), 2007
2006
Predictor@Home: A "Protein Structure Prediction Supercomputer' Based on Global Computing.
IEEE Trans. Parallel Distributed Syst., 2006
2005
Detailed considerations for a balanced and broadly applicable force field: A study of substituted benzenes modeled with OPLS-AA.
J. Comput. Chem., 2005
Application of torsion angle molecular dynamics for efficient sampling of protein conformations.
J. Comput. Chem., 2005
Study of a highly accurate and fast protein-ligand docking method based on molecular dynamics.
Concurr. Comput. Pract. Exp., 2005
Predictor@Home: A "Protein Structure Prediction Supercomputer" Based on Public-Resource Computing.
Proceedings of the 19th International Parallel and Distributed Processing Symposium (IPDPS 2005), 2005
Homogeneous Redundancy: a Technique to Ensure Integrity of Molecular Simulation Results Using Public Computing.
Proceedings of the 19th International Parallel and Distributed Processing Symposium (IPDPS 2005), 2005
Proceedings of the First International Conference on e-Science and Grid Technologies (e-Science 2005), 2005
2004
CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.
J. Comput. Chem., 2004
CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations.
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.
J. Comput. Chem., 2004
Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations.
J. Comput. Chem., 2004
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures.
J. Comput. Chem., 2004
Studying protein folding on the Grid: experiences using CHARMM on NPACI resources under Legion.
Concurr. Comput. Pract. Exp., 2004
Study of a Highly Accurate and Fast Protein-Ligand Docking Algorithm Based on Molecular Dynamics.
Proceedings of the 18th International Parallel and Distributed Processing Symposium (IPDPS 2004), 2004
Proceedings of the 18th International Parallel and Distributed Processing Symposium (IPDPS 2004), 2004
2003
Detailed analysis of grid-based molecular docking: A case study of CDOCKER - A CHARMm-based MD docking algorithm.
J. Comput. Chem., 2003
New analytic approximation to the standard molecular volume definition and its application to generalized born calculations - Erratum.
J. Comput. Chem., 2003
New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.
J. Comput. Chem., 2003
J. Comput. Aided Mol. Des., 2003
2002
J. Comput. Chem., 2002
J. Comput. Chem., 2002
1998
1995
J. Comput. Chem., 1995
1994
Implementation of a Data Parallel, Logical Domain Decomposition Method for Interparticle Interactions in Molecular Dynamics of Structured Molecular Fluids.
J. Comput. Chem., 1994
1991