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Chemistry

D-Index
116
Citations
68467
World Ranking
579
National Ranking
245

Overview

Charles L. Brooks is affiliated with the University of Michigan-Ann Arbor in the United States. Their research primarily spans the field of Biochemistry, Genetics, and Molecular Biology, with a focus on several subfields including Molecular Biology, Materials Chemistry, Computational Theory and Mathematics, Organic Chemistry, and Spectroscopy.

The scientist's work concentrates on key topics such as Protein Structure and Dynamics, Enzyme Structure and Function, Computational Drug Discovery Methods, RNA and protein synthesis mechanisms, Microbial Natural Products and Biosynthesis, Spectroscopy and Quantum Chemical Studies, and Enzyme Catalysis and Immobilization.

Frequent publication venues where Charles L. Brooks has contributed include:

  • Journal of Chemical Theory and Computation
  • Journal of Chemical Information and Modeling
  • bioRxiv (Cold Spring Harbor Laboratory)
  • The Journal of Physical Chemistry B
  • Proceedings of the National Academy of Sciences

Some of the recent papers authored or co-authored by this researcher are:

  • Automated, Accurate, and Scalable Relative Protein-Ligand Binding Free-Energy Calculations Using Lambda Dynamics, 2020, Journal of Chemical Theory and Computation
  • Accelerated CDOCKER with GPUs, Parallel Simulated Annealing, and Fast Fourier Transforms, 2020, Journal of Chemical Theory and Computation
  • CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed, 2024, The Journal of Physical Chemistry B
  • Classical molecular dynamics, 2021, The Journal of Chemical Physics
  • BLaDE: A Basic Lambda Dynamics Engine for GPU-Accelerated Molecular Dynamics Free Energy Calculations, 2021, Journal of Chemical Theory and Computation

Frequent co-authors who have collaborated with Charles L. Brooks include:

  • Ryan L. Hayes
  • Yujin Wu
  • Jonah Z. Vilseck
  • Luis F. Cervantes
  • Azam Hussain

Best Publications

  • CHARMM: the biomolecular simulation program.

    B. R. Brooks;C. L. Brooks;A. D. Mackerell;L. Nilsson

  • CHARMM-GUI Input Generator for NAMD, Gromacs, Amber, Openmm, and CHARMM/OpenMM Simulations using the CHARMM36 Additive Force Field

    Jumin Lee;Xi Cheng;Jason M. Swails;Min Sun Yeom

  • 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.

    Alexander D. Mackerell;Michael Feig;Charles L. Brooks

  • Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm.

    Guosheng Wu;Daniel H. Robertson;Charles L. Brooks;Michal Vieth

  • A modified TIP3P water potential for simulation with Ewald summation.

    Daniel J. Price;Charles L. Brooks

  • Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics

    C. L. Brooks;M. Karplus;B. Montgomery Pettitt;Robert H. Austin

  • Improved treatment of the protein backbone in empirical force fields.

    Alexander D. MacKerell;Michael Feig;Charles L. Brooks

  • MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology

    Michael Feig;John Karanicolas;Charles L. Brooks

  • CHARMM: The Energy Function and Its Parameterization

    Alexander D. MacKerell;Bernard Brooks;Charles L. Brooks;Lennart Nilsson

  • Generalized born model with a simple smoothing function

    Wonpil Im;Michael S. Lee;Charles L. Brooks

  • Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures.

    Michael Feig;Alexey Onufriev;Michael S. Lee;Wonpil Im

  • Stochastic boundary conditions for molecular dynamics simulations of ST2 water

    Axel Brünger;Charles L. Brooks;Martin Karplus

  • Recent advances in the development and application of implicit solvent models in biomolecule simulations.

    Michael Feig;Charles L Brooks

  • From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding.

    Joan-Emma Shea;Charles L. Brooks

  • Deformable stochastic boundaries in molecular dynamics

    C. L. Brooks;Martin Karplus

  • New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.

    Michael S. Lee;Michael Feig;Freddie R. Salsbury;Charles L. Brooks

  • Assessing scoring functions for protein-ligand interactions.

    Philippe Ferrara;Holger Gohlke;Daniel J. Price;Gerhard Klebe

  • CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules

    Seonghoon Kim;Jumin Lee;Sunhwan Jo;Charles L. Brooks

  • CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations.

    Sandeep Patel;Charles L. Brooks

  • Novel generalized Born methods

    Michael S. Lee;Freddie R. Salsbury;Charles L. Brooks

  • Computer simulation of liquids

    Charles L. Brooks

Frequent Co-Authors

Michael Feig
Michael Feig Michigan State University
Martin Karplus
Martin Karplus Harvard University
Hashim M. Al-Hashimi
Hashim M. Al-Hashimi Duke University
Wonpil Im
Wonpil Im Lehigh University
Douglas J. Tobias
Douglas J. Tobias University of California, Irvine
Zhan Chen
Zhan Chen University of Michigan–Ann Arbor
Andrzej Kolinski
Andrzej Kolinski University of Warsaw
Jeffrey Skolnick
Jeffrey Skolnick Georgia Institute of Technology
Darrell G. Schlom
Darrell G. Schlom Cornell University
Michael F. Crowley
Michael F. Crowley National Renewable Energy Laboratory

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