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1

FROM FOLDING THEORIES TO FOLDING PROTEINS: A Review and Assessment of Simulation Studies of Protein Folding and Unfolding

Shea, Joan-Emma, Brooks III, Charles L

Journal:

Annual Review of Physical Chemistry

Year:

2001

Language:

english

File:

PDF, 917 KB

english, 2001

2

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

Sandeep Patel, Charles L. Brooks III

Journal:

Journal of Computational Chemistry

Year:

2004

Language:

english

File:

PDF, 267 KB

english, 2004

3

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 Jr., Michael Feig, Charles L. Brooks III

Journal:

Journal of Computational Chemistry

Year:

2004

Language:

english

File:

PDF, 462 KB

english, 2004

4

CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model

Sandeep Patel, Alexander D. Mackerell Jr., Charles L. Brooks III

Journal:

Journal of Computational Chemistry

Year:

2004

Language:

english

File:

PDF, 416 KB

english, 2004

5

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

Michael Feig, John Karanicolas, Charles L. Brooks III

Journal:

Journal of Molecular Graphics and Modelling

Year:

2004

Language:

english

File:

PDF, 768 KB

english, 2004

6

Curious structure in “canonical” alanine-based peptides

William A. Shirley, Charles L. Brooks III

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1997

Language:

english

File:

PDF, 263 KB

english, 1997

7

A molecular dynamics simulation study of segment B1 of protein G

Felix B. Sheinerman, Charles L. Brooks III

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1997

Language:

english

File:

PDF, 183 KB

english, 1997

8

Correlation between knowledge-based and detailed atomic potentials: Application to the unfolding of the GCN4 leucine zipper

Debasisa Mohanty, Brian N. Dominy, Andrzej Kolinski, Charles L. Brooks III, Jeffrey Skolnick

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 107 KB

english, 1999

9

Methodology for protein–ligand binding studies: Application to a model for drug resistance, the HIV/FIV protease system

Brian N. Dominy, Charles L. Brooks III

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 155 KB

english, 1999

10

Thermodynamics of protein folding: A statistical mechanical study of a small all-β protein

Zhuyan Guo, Charles L. Brooks III

Journal:

Year:

1997

Language:

english

File:

PDF, 160 KB

english, 1997

11

Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models

Michael Feig, Piotr Rotkiewicz, Andrzej Kolinski, Jeffrey Skolnick, Charles L. Brooks III

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2000

Language:

english

File:

PDF, 305 KB

english, 2000

12

Ribosome motions modulate electrostatic properties

Joanna Trylska, Robert Konecny, Florence Tama, Charles L. Brooks III, J. Andrew McCammon

Journal:

Year:

2004

Language:

english

File:

PDF, 550 KB

english, 2004

13

Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids

Robert Konecny, Joanna Trylska, Florence Tama, Deqiang Zhang, Nathan A. Baker, Charles L. Brooks III, J. A. McCammon

Journal:

Year:

2006

Language:

english

File:

PDF, 695 KB

english, 2006

14

Virtual rigid body dynamics

Teresa Head-Cordon, Charles L. Brooks III

Journal:

Year:

1991

Language:

english

File:

PDF, 1.96 MB

english, 1991

15

ChemInform Abstract: Evolution and Physics in Comparative Protein Structure Modeling

Andras Fiser, Michael Feig, Charles L. Brooks III, Andrej Sali

Journal:

Year:

2002

File:

PDF, 24 KB

2002

16

ChemInform Abstract: Protein and Peptide Folding Explored with Molecular Simulations

Charles L. Brooks III

Journal:

Year:

2002

File:

PDF, 24 KB

2002

17

Studying protein folding on the Grid: experiences using CHARMM on NPACI resources under Legion

Anand Natrajan, Michael Crowley, Nancy Wilkins-Diehr, Marty A. Humphrey, Anthony D. Fox, Andrew S. Grimshaw, Charles L. Brooks III

Journal:

Concurrency and Computation: Practice and Experience

Year:

2004

Language:

english

File:

PDF, 277 KB

english, 2004

18

Temperature-Dependent Behavior of Protein-Chromophore Interactions: A Theoretical Study of a Blue Fluorescent Antibody

Freddie R. Salsbury Jr., Wen-Ge Han, Louis Noodleman, Charles L. Brooks III

Journal:

Year:

2003

Language:

english

File:

PDF, 155 KB

english, 2003

19

Identifying native-like protein structures using physics-based potentials

Brian N. Dominy, Charles L. Brooks, III

Journal:

Journal of Computational Chemistry

Year:

2002

Language:

english

File:

PDF, 251 KB

english, 2002

20

Modern protein force fields behave comparably in molecular dynamics simulations

Daniel J. Price, Charles L. Brooks III

Journal:

Journal of Computational Chemistry

Year:

2002

Language:

english

File:

PDF, 596 KB

english, 2002

21

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

Michael S. Lee, Michael Feig, Freddie R. Salsbury Jr., Charles L. Brooks III

Journal:

Journal of Computational Chemistry

Year:

2003

Language:

english

File:

PDF, 153 KB

english, 2003

22

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 III, Michal Vieth

Journal:

Journal of Computational Chemistry

Year:

2003

Language:

english

File:

PDF, 333 KB

english, 2003

23

Generalized born model with a simple smoothing function

Wonpil Im, Michael S. Lee, Charles L. Brooks III

Journal:

Journal of Computational Chemistry

Year:

2003

Language:

english

File:

PDF, 272 KB

english, 2003

24

New analytic approximation to the standard molecular volume definition and its application to generalized born calculations

Michael S. Lee, Michael Feig, Freddie R. Salsbury Jr., Charles L. Brooks III

Journal:

Journal of Computational Chemistry

Year:

2003

File:

PDF, 38 KB

2003

25

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, David A. Case, Charles L. Brooks III

Journal:

Journal of Computational Chemistry

Year:

2004

Language:

english

File:

PDF, 205 KB

english, 2004

26

Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations

Olgun Guvench, Charles L. Brooks III

Journal:

Journal of Computational Chemistry

Year:

2004

Language:

english

File:

PDF, 485 KB

english, 2004

27

Detailed considerations for a balanced and broadly applicable force field: A study of substituted benzenes modeled with OPLS-AA

Daniel J. Price, Charles L. Brooks III

Journal:

Journal of Computational Chemistry

Year:

2005

Language:

english

File:

PDF, 149 KB

english, 2005

28

Application of torsion angle molecular dynamics for efficient sampling of protein conformations

Jianhan Chen, Wonpil Im, Charles L. Brooks III

Journal:

Journal of Computational Chemistry

Year:

2005

Language:

english

File:

PDF, 542 KB

english, 2005

29

Editorial

Charles L. Brooks III

Journal:

Journal of Computational Chemistry

Year:

2005

Language:

english

File:

PDF, 25 KB

english, 2005

30

Letter from the Editors

Charles L. Brooks III, Gernot Frenking, Shigeyoshi Sakaki

Journal:

Journal of Computational Chemistry

Year:

2007

Language:

english

File:

PDF, 27 KB

english, 2007

31

Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions

Mark A. Olson, Michael Feig, Charles L. Brooks III

Journal:

Journal of Computational Chemistry

Year:

2008

Language:

english

File:

PDF, 1.01 MB

english, 2008

32

Editors' note

Gernot Frenking, Charles L. Brooks III, Shigeyoshi Sakiki

Journal:

Journal of Computational Chemistry

Year:

2009

Language:

english

File:

PDF, 25 KB

english, 2009

33

λ-Dynamics free energy simulation methods

Jennifer L. Knight, Charles L. Brooks III

Journal:

Journal of Computational Chemistry

Year:

2009

Language:

english

File:

PDF, 134 KB

english, 2009

34

Surveying implicit solvent models for estimating small molecule absolute hydration free energies

Jennifer L. Knight, Charles L. Brooks III

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 530 KB

english, 2011

35

Applying efficient implicit nongeometric constraints in alchemical free energy simulations

Jennifer L. Knight, Charles L. Brooks III

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 457 KB

english, 2011

36

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

Joseph D. Yesselman, Daniel J. Price, Jennifer L. Knight, Charles L. Brooks III

Journal:

Journal of Computational Chemistry

Year:

2012

Language:

english

File:

PDF, 857 KB

english, 2012

37

Vector and parallel algorithms for the molecular dynamics simulation of macromolecules on shared-memory computers

John E. Mertz, Douglas J. Tobias, Charles L. Brooks III, U. C. Singh

Journal:

Journal of Computational Chemistry

Year:

1991

Language:

english

File:

PDF, 797 KB

english, 1991

38

Implementation of a data parallel, logical domain decomposition method for interparticle interactions in molecular dynamics of structured molecular fluids

William S. Young, Charles L. Brooks III

Journal:

Journal of Computational Chemistry

Year:

1994

Language:

english

File:

PDF, 828 KB

english, 1994

39

Dynamic load balancing algorithms for replicated data molecular dynamics

William S. Young, Charles L. Brooks III

Journal:

Journal of Computational Chemistry

Year:

1995

Language:

english

File:

PDF, 755 KB

english, 1995

40

A Mechanism for Evolving Novel Plant Sesquiterpene Synthase Function

Troy Wymore, Brian Y. Chen, Hugh B. Nicholas Jr., Alexander J. Ropelewski, Charles L. Brooks III

Journal:

Molecular Informatics

Year:

2011

Language:

english

File:

PDF, 1.15 MB

english, 2011

41

Stochastic boundary conditions for molecular dynamics simulations of ST2 water

Axel Brünger, Charles L. Brooks III, Martin Karplus

Journal:

Chemical Physics Letters

Year:

1984

Language:

english

File:

PDF, 550 KB

english, 1984

42

Calculation of free energy surfaces using the methods of thermodynamic perturbation theory

Douglas J. Tobias, Charles L. Brooks III

Journal:

Chemical Physics Letters

Year:

1987

Language:

english

File:

PDF, 455 KB

english, 1987

43

Computational simulations of the Trichoderma reesei cellobiohydrolase I acting on microcrystalline cellulose Iβ: the enzyme–substrate complex

Linghao Zhong, James F. Matthews, Peter I. Hansen, Michael F. Crowley, Joseph M. Cleary, Ross C. Walker, Mark R. Nimlos, Charles L. Brooks III, William S. Adney, Michael E. Himmel, John W. Brady

Journal:

Carbohydrate Research

Year:

2009

Language:

english

File:

PDF, 1.70 MB

english, 2009

44

Application of solid-state NMR restraint potentials in membrane protein modeling

Jinhyuk Lee, Jianhan Chen, Charles L. Brooks III, Wonpil Im

Journal:

Journal of Magnetic Resonance

Year:

2008

Language:

english

File:

PDF, 1.02 MB

english, 2008

45

Conformational flexibility in free energy simulations

Douglas J. Tobias, Charles L. Brooks III, Stephen H. Fleischman

Journal:

Chemical Physics Letters

Year:

1989

Language:

english

File:

PDF, 451 KB

english, 1989

46

Evaluating CASP4 predictions with physical energy functions

Michael Feig, Charles L. Brooks III

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2002

Language:

english

File:

PDF, 261 KB

english, 2002

47

The importance of explicit chain representation in protein folding models: An examination of ising-like models

John Karanicolas, Charles L. Brooks III

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 338 KB

english, 2003

48

Modeling of the metallo-β-lactamase from B. fragilis: Structural and dynamic effects of inhibitor binding

Freddie R. Salsbury Jr., Michael F. Crowley, Charles L. Brooks III

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2001

Language:

english

File:

PDF, 542 KB

english, 2001

49

Constant-pH molecular dynamics using continuous titration coordinates

Michael S. Lee, Freddie R. Salsbury Jr., Charles L. Brooks III

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 203 KB

english, 2004

50

An electrostatic basis for the stability of thermophilic proteins

Brian N. Dominy, Hervé Minoux, Charles L. Brooks III

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 527 KB

english, 2004

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