Charles L. Brooks III

Orcid: 0000-0002-8149-5417

Affiliations:
  • University of Michigan, Department of Chemistry, Ann Arbor, USA


According to our database1, Charles L. Brooks III authored at least 67 papers between 1991 and 2024.

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Bibliography

2024
Investigating Polypharmacology through Targeting Known Human Neutrophil Elastase Inhibitors to Proteinase 3.
J. Chem. Inf. Model., 2024

Exploring the Limits of the Generalized CHARMM and AMBER Force Fields through Predictions of Hydration Free Energy of Small Molecules.
J. Chem. Inf. Model., 2024

2023
FASTDock: A Pipeline for Allosteric Drug Discovery.
J. Chem. Inf. Model., November, 2023

2022
Allostery in the dynamic coactivator domain KIX occurs through minor conformational micro-states.
PLoS Comput. Biol., 2022

Optimizing Multisite λ-Dynamics Throughput with Charge Renormalization.
J. Chem. Inf. Model., 2022

Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4.
J. Chem. Inf. Model., 2022

Covalent docking in CDOCKER.
J. Comput. Aided Mol. Des., 2022

2021
VIPERdb v3.0: a structure-based data analytics platform for viral capsids.
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
CDOCKER and λ-dynamics for prospective prediction in D3R Grand Challenge 2.
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

Coupled folding and binding with 2D Window-Exchange Umbrella Sampling.
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

Viral Capsid Proteins Are Segregated in Structural Fold Space.
PLoS Comput. Biol., 2013

Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes.
J. Comput. Chem., 2013

New paint and a new engine.
J. Comput. Chem., 2013

2012
A Universal Trend among Proteomes Indicates an Oily Last Common Ancestor.
PLoS Comput. Biol., 2012

MATCH: An atom-typing toolset for molecular mechanics force fields.
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

lambda-Dynamics free energy simulation methods.
J. Comput. Chem., 2009

Editors' note.
J. Comput. Chem., 2009

CHARMM: The biomolecular simulation program.
J. Comput. Chem., 2009

De novo modeling of GPCR class A structures.
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
Deprotonation by Dehydration: The Origin of Ammonium Sensing in the AmtB Channel.
PLoS Comput. Biol., 2007

Letter from the Editors.
J. Comput. Chem., 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

VIPERdb: a relational database for structural virology.
Nucleic Acids Res., 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

Editorial.
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

Metrics for Effective Resource Management in Global Computing Environments.
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

Characterizing and Evaluating Desktop Grids: An Empirical Study.
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

Generalized born model with a simple smoothing function.
J. Comput. Chem., 2003

Comparative study of several algorithms for flexible ligand docking.
J. Comput. Aided Mol. Des., 2003

2002
Modern protein force fields behave comparably in molecular dynamics simulations.
J. Comput. Chem., 2002

Identifying native-like protein structures using physics-based potentials.
J. Comput. Chem., 2002

1998
Assessing energy functions for flexible docking.
J. Comput. Chem., 1998

Assessing search strategies for flexible docking.
J. Comput. Chem., 1998

1995
Dynamic Load Balancing Algorithms for Replicated Data Molecular Dynamics.
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
Molecular Simulations On Supercomputers.
Int. J. High Perform. Comput. Appl., 1991


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