C. Brooks

发表

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

Charles L. Brooks, Olgun Guvench, Olgun Guvench, 2004, J. Comput. Chem..

Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.

C. Brooks, F. Tama, 2006, Annual review of biophysics and biomolecular structure.

Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis.

C. Brooks, F. Tama, 2005, Journal of molecular biology.

Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV.

C. Brooks, C. Brooks, M. E. Karpen, 1993, Biochemistry.

Assessing scoring functions for protein-ligand interactions.

D. J. Price, G. Klebe, C. Brooks, 2004, Journal of medicinal chemistry.

Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling

C. Brooks, H. Dyson, Jianhan Chen, 2005, Journal of biomolecular NMR.

An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins.

C. Brooks, W. Im, M. Feig, 2003, Biophysical journal.

De novo folding of membrane proteins: an exploration of the structure and NMR properties of the fd coat protein.

C. Brooks, W. Im, 2004, Journal of molecular biology.

Improved treatment of the protein backbone in empirical force fields.

Alexander D. MacKerell, C. Brooks, M. Feig, 2004, Journal of the American Chemical Society.

Constant-temperature free energy surfaces for physical and chemical processes

C. Brooks, E. Boczko, 1993 .

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

C. Brooks, J. Shea, J. Shea, 2001, Annual review of physical chemistry.

Viewing protein folding from many perspectives

C. Brooks, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Novel generalized Born methods

C. Brooks, Michael S. Lee, F. Salsbury, 2002 .

Constant‐pH molecular dynamics using continuous titration coordinates

C. Brooks, Michael S. Lee, F. Salsbury, 2004, Proteins.

Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models.

C. Brooks, Jianhan Chen, W. Im, 2005, Advances in protein chemistry.

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

C. Brooks, M. Feig, 2004, Current opinion in structural biology.

Constant pH molecular dynamics with proton tautomerism.

C. Brooks, Jana Khandogin, 2005, Biophysical journal.

Advances in chemical physics, volume 71: Proteins: A theoretical perspective of dynamics, structure, and thermodynamics

M. Karplus, C. Brooks, B. Pettitt, 2006 .

Deformable stochastic boundaries in molecular dynamics

M. Karplus, C. Brooks, 1983 .

Charles L Brooks, C. Brooks, T. Rod, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Taking a Walk on a Landscape

C L Brooks, J. Onuchic, D. Wales, 2001, Science.

Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids

B. Montgomery Pettitt, Charles L. Brooks, Martin Karplus, 1985 .

First-principles calculation of the folding free energy of a three-helix bundle protein.

C. Brooks, E. Boczko, EM Boczko, 1995, Science.

Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A.

C L Brooks, J. Onuchic, C. Brooks, 1999, Proceedings of the National Academy of Sciences of the United States of America.

Thermodynamics and mechanism of alpha helix initiation in alanine and valine peptides.

C. Brooks, D. Tobias, 1991, Biochemistry.

An electrostatic basis for the stability of thermophilic proteins

Hervé Minoux, Charles L Brooks, C. Brooks, 2004, Proteins.

How to improve nature: study of the electrostatic properties of the surface of α-lactalbumin

Charles L. Brooks, Vladimir N. Uversky, Lawrence J. Berliner, 2005 .

The effects of ionic strength on protein stability: the cold shock protein family.

Charles L Brooks, C. Brooks, D. Perl, 2002, Journal of molecular biology.

Albumin binding to FcRn: distinct from the FcRn-IgG interaction.

Charles L Brooks, C. Brooks, C. Chaudhury, 2006, Biochemistry.

The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus.

Florence Tama, Charles L Brooks, C. Brooks, 2002, Journal of molecular biology.

Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions.

Charles L Brooks, Jianhan Chen, C. Brooks, 2008, Physical chemistry chemical physics : PCCP.

Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics

Charles L. Brooks, Ronald D. Hills, C. Brooks, 2009, International journal of molecular sciences.

The origins of asymmetry in the folding transition states of protein L and protein G

John Karanicolas, Charles L Brooks, J. Karanicolas, 2002, Protein science : a publication of the Protein Society.

Probing the folding free energy landscape of the src-SH3 protein domain

Joan-Emma Shea, Charles L Brooks, J. Onuchic, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Statistical determinants of selective ionic complexation: ions in solvent, transport proteins, and other "hosts".

C. Brooks, D. Bostick, 2009, Biophysical journal.

Exploring the folding free energy surface of a three-helix bundle protein.

C. Brooks, E. Boczko, Z. Guo, 1997, Proceedings of the National Academy of Sciences of the United States of America.

A modified TIP3P water potential for simulation with Ewald summation.

D. J. Price, C. Brooks, 2004, The Journal of chemical physics.

Nanosecond time scale folding dynamics of a pentapeptide in water.

C. Brooks, J. Mertz, D. Tobias, 1991, Biochemistry.

Folding Free Energy Surface of a Three-Stranded β-Sheet Protein

C. Brooks, B. Bursulaya, 1999 .

Comparative Study of the Folding Free Energy Landscape of a Three-Stranded β-Sheet Protein with Explicit and Implicit Solvent Models

C. Brooks, Badry D. Bursulaya and, 2000 .

Exploring Flory's isolated-pair hypothesis: Statistical mechanics of helix–coil transitions in polyalanine and the C-peptide from RNase A

C. Brooks, Y. Ohkubo, 2003, Proceedings of the National Academy of Sciences of the United States of America.

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

C. Brooks, Z. Guo, Z. Guo, 1997 .

Molecular dynamics simulations of isolated helices of myoglobin.

C. Brooks, J. Hirst, Jonathan D. Hirst, 1995, Biochemistry.

FoldGPCR: Structure prediction protocol for the transmembrane domain of G protein‐coupled receptors from class A

R. Stevens, C. Brooks, Jianhan Chen, 2010, Proteins.

Do active site conformations of small ligands correspond to low free-energy solution structures?

C L Brooks, J D Hirst, C. Brooks, 1998, Journal of computer-aided molecular design.

Fluctuating charge force fields: recent developments and applications from small molecules to macromolecular biological systems

Charles L. Brooks, Sandeep Patel, C. Brooks, 2006 .

Recent advances in implicit solvent-based methods for biomolecular simulations.

Charles L Brooks, Jianhan Chen, C. Brooks, 2008, Current opinion in structural biology.

Ligand-protein database: linking protein-ligand complex structures to binding data.

C L Brooks, C. Brooks, O. Roche, 2001, Journal of medicinal chemistry.

Simulations of peptide conformational dynamics and thermodynamics

Charles L. Brooks, David A. Case, D. Case, 1993 .

CHARGE SCREENING AND THE DIELECTRIC CONSTANT OF PROTEINS : INSIGHTS FROM MOLECULAR DYNAMICS

Charles L. Brooks, C. Brooks, and Thomas Simonson, 1996 .

Toward the accurate first-principles prediction of ionization equilibria in proteins.

Charles L Brooks, C. Brooks, Jana Khandogin, 2006, Biochemistry.

Improved model building and assessment of the Calcium‐sensing receptor transmembrane domain

Mayako Michino, Charles L Brooks, C. Brooks, 2008, Proteins.

Receptor rigidity and ligand mobility in trypsin–ligand complexes

Olgun Guvench, Charles L Brooks, D. J. Price, 2005, Proteins.

Prediction of the folding pathways and structure of the GCN4 leucine zipper.

A Kolinski, J Skolnick, C L Brooks, 1994, Journal of molecular biology.

Protein and peptide folding explored with molecular simulations.

Charles L Brooks, C. Brooks, 2002, Accounts of chemical research.

Characterization of "native" apomyoglobin by molecular dynamics simulation.

C L Brooks, C. Brooks, Charles L. Brooks, 1992, Journal of molecular biology.

Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme.

M Karplus, C L Brooks, M. Karplus, 1989, Journal of molecular biology.

A line integral reaction path approximation for large systems via nonlinear constrained optimization: application to alanine dipeptide and the beta hairpin of protein G.

R. Byrd, C. Brooks, I. Khavrutskii, 2006, The Journal of chemical physics.

Evolution and physics in comparative protein structure modeling.

A. Sali, C. Brooks, A. Fiser, 2002, Accounts of chemical research.

Evolution and Physics in Comparative Protein Structure Modeling

Charles L. Brooks, Andrej Sali, Andras Fiser, 2002 .

Molecular Simulations of Protein Structure, Dynamics and Thermodynamics

C. Brooks, 1990 .

A microscopic view of helix propagation: N and C-terminal helix growth in alanine helices.

C L Brooks, C. Brooks, W S Young, 1996, Journal of molecular biology.

A survey of calmodulin-activated protein kinase activity in several tissues of Rattus rattus.

C. Brooks, J. McDonald, M. Landt, 1982, Comparative biochemistry and physiology. B, Comparative biochemistry.

A method for predicting protein structure from sequence

Adam Godzik, Andrzej Kolinski, Jeffrey Skolnick, 1993, Current Biology.

Force field influence on the observation of π-helical protein structures in molecular dynamics simulations

Alexander D. MacKerell, Charles L. Brooks, Michael Feig, 2003 .

Assessing energy functions for flexible docking

Charles L. Brooks, Jonathan D. Hirst, Michal Vieth, 1998, J. Comput. Chem..

Are Many-Body Effects Important in Protein Folding?

Charles L. Brooks, Kenneth M. Merz, Arjan van der Vaart, 2000 .

Free energy screening of small ligands binding to an artificial protein cavity

Charles L. Brooks, Shinichi Banba, C. Brooks, 2000 .

The role of electrostatics in the binding of small ligands to enzymes

Charles L. Brooks, Teresa Head-Gordon, C. Brooks, 1987 .

Effects of storage on serum ionized calcium and pH from horses with normal and abnormal ionized calcium concentrations.

C. Brooks, P. Schenck, D. Chew, 1996, Veterinary clinical pathology.

Active site dynamics of ribonuclease.

M Karplus, C L Brooks, A T Brünger, 1985, Proceedings of the National Academy of Sciences of the United States of America.

Alloxan inhibition of a Ca2+- and calmodulin-dependent protein kinase activity in pancreatic islets.

P. Lacy, M. Mcdaniel, C. Brooks, 1983, Journal of Biological Chemistry.

Obligate Ordered Binding of Human Lactogenic Cytokines*

Charles L Brooks, C. Brooks, Jeffery L Voorhees, 2010, The Journal of Biological Chemistry.

Zinc binding to human lactogenic hormones and the human prolactin receptor

C. Brooks, J. L. Voorhees, G. V. Rao, 2011, FEBS letters.

pH‐induced transition and Zn2+‐binding properties of bovine prolactin 1

C. Brooks, G. Deikus, D. Veprintsev, 1997, FEBS letters.

Human growth hormone site 2 lactogenic activity requires a distant tyrosine164

C. Brooks, K. Duda, 1999, FEBS letters.

Expression, folding, and characterization of small proteins with increasing disulfide complexity by a pT7-7-derived phagemid.

P. J. Anderson, C. Brooks, L. Berliner, 1999, Protein expression and purification.

Differential effects of zinc on functionally distinct human growth hormone mutations.

C. Brooks, K. Duda, 2003, Protein engineering.

The influence of geometrical fluctuations on electron tunneling barriers in proteins

C. Brooks, S. Sneddon, 1988 .

Improved Gō-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions.

John Karanicolas, Charles L Brooks, J. Karanicolas, 2003, Journal of molecular biology.

Identification of a Motif Associated with the Lactogenic Actions of Human Growth Hormone*

C. Brooks, F. Peterson, 1997, The Journal of Biological Chemistry.

Biological activity of phosphorylated and dephosphorylated bovine prolactin

C. Brooks, J. Wicks, 1995, Molecular and Cellular Endocrinology.

Selective complexation of K+ and Na+ in simple polarizable ion-ligating systems.

C. Brooks, C. Brooks, D. Bostick, 2010, Journal of the American Chemical Society.

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

Charles L. Brooks, Daniel J. Price, C. Brooks, 2005, J. Comput. Chem..

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

Charles L. Brooks, Daniel J. Price, Jennifer L. Knight, 2012, J. Comput. Chem..

Correlation of Ca2+-and calmodulin-dependent protein kinase activity with secretion of insulin from islets of Langerhans.

M. Mcdaniel, C. Brooks, J. Colca, 1983, The Biochemical journal.

Site-specific spectroscopic measurement of spin and charge in (LuFeO3)m/(LuFe2O4)1 multiferroic superlattices

Kevin A. Smith, D. Muller, C. Fennie, 2020, Nature Communications.

Inhibition of mammary tumorigenesis in carcinogen-treated Lewis rats by suppression of prolactin secretion.

C. Brooks, B. Denenberg, C. Welsch, 1979, Journal of the National Cancer Institute.

Computational Multiscale Modeling in

Patricia J. Teller, Michela Taufer, Roger S. Armen, 2009 .

Calmodulin-dependent protein kinase in acini from lactating rat mammary tissue: subcellular locale, characterization, and solubilization.

C. Brooks, M. Landt, 1985, Archives of biochemistry and biophysics.

Specificity of inhibition of calcium- and calmodulin-dependent protein kinase by alloxan.

M. Mcdaniel, C. Brooks, J. Colca, 1984, Biochimica et biophysica acta.

Functional relationship of serine 90 phosphorylation and the surrounding putative salt bridge in bovine prolactin

C. Brooks, E. Schenck, J. Canfield, 2003, Molecular and Cellular Endocrinology.

Zinc binding in bovine α‐lactalbumin: Sequence homology may not be a predictor of subtle functional features

C. Brooks, L. Berliner, D. Veprintsev, 2000, Proteins.

Fine tuning the N‐terminus of a calcium binding protein: α‐lactalbumin

C. Brooks, L. Berliner, V. Uversky, 1999 .

The metabolism and nuclear migration of estrogen in porcine uterus throughout the implantation process.

C. Brooks, S. Brooks, W. Dukelow, 1979, Biology of reproduction.

On the equivalence point for ammonium (de)protonation during its transport through the AmtB channel.

C. Brooks, D. Bostick, 2007, Biophysical journal.

17beta-oestradiol and Enovid mammary tumorigenesis in C3H/HeJ female mice: counteraction by concurrent 2-bromo-alpha-ergocryptine.

C. Brooks, C. Welsch, C. Adams, 1977, British Journal of Cancer.

Prolactin kinase activity in bovine anterior pituitary sub-cellular fractions

C. Brooks, J. Wicks, 1999, Molecular and Cellular Endocrinology.

Detailed analysis of grid‐based molecular docking: A case study of CDOCKER—A CHARMm‐based MD docking algorithm

Charles L. Brooks, Guosheng Wu, Michal Vieth, 2003, J. Comput. Chem..

The Stability of Protein Secondary Structures in Aqueous Solution

C. Brooks, D. Tobias, S. Sneddon, 2008 .

Effect of an interfering substance on determination of potassium by ion-specific potentiometry in animal urine.

C. Brooks, F. Garry, M. Swartout, 1988, American journal of veterinary research.

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, Charles L. Brooks, Michael Feig, 2004, J. Comput. Chem..

Generalized born model with a simple smoothing function

Charles L. Brooks, Wonpil Im, Michael S. Lee, 2003, J. Comput. Chem..

Synthesis and screening of a cyclic peptide library: discovery of small-molecule ligands against human prolactin receptor.

Charles L Brooks, Sang Hoon Joo, C. Brooks, 2009, Bioorganic & medicinal chemistry.

Comparative study of several algorithms for flexible ligand docking

Ruben Abagyan, Maxim Totrov, Charles L. Brooks, 2003, J. Comput. Aided Mol. Des..

Toxic Effects of Butylated Triphenyl Phosphate-based Hydraulic Fluid and Tricresyl Phosphate in Female F344 Rats

C L Brooks, C. Brooks, C. Capen, 1995, Veterinary pathology.

Multireference Configuration Interaction Calculations of Electronic States ofN-Methylformamide, Acetamide, andN-Methylacetamide

D. M. Hirst, C. Brooks, J. Hirst, 1997 .

Stability of a model β-sheet in water

Charles L. Brooks, Douglas J. Tobias, C. Brooks, 1992 .

Dynamics of liquid state chemical reactions: Photodissociation dynamics and geminate recombination of molecular iodine in liquid solution

C. Brooks, S. Adelman, Michael W. Balk, 1983 .

Dynamics of liquid state chemical reactions: R‐dependent correlation functions for I.+I. in CCl4

C. Brooks, S. Adelman, 1982 .

Enhanced immunogenicity of a conformational epitope of human T-lymphotropic virus type 1 using a novel chimeric peptide.

C. Brooks, M. Lairmore, S. Schwendeman, 2000, Vaccine.

The requirement for mechanical coupling between head and S2 domains in smooth muscle myosin ATPase regulation and its implications for dimeric motor function.

Florence Tama, Michael Feig, Charles L Brooks, 2005, Journal of molecular biology.

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

Michael Feig, John Karanicolas, Charles L Brooks, 2004, Journal of molecular graphics & modelling.

Functional identification of calcium binding residues in bovine alpha-lactalbumin.

P. J. Anderson, C. Brooks, L. Berliner, 1997, Biochemistry.

Effects of storage on serum ionized calcium and pH values in clinically normal dogs.

C. Brooks, P. Schenck, D. Chew, 1995, American journal of veterinary research.

A nine-base nucleotide sequence in the porcine circovirus type 2 (PCV2) nucleocapsid gene determines viral replication and virulence.

C. Brooks, J. Ellis, E. Kaufmann, 2012, Virus research.

Dioxygen-bridged and monomeric cobalt(III) complexes with 1,3-Diamino-2-(aminomethyl) propane and ethylenediamine

C. Brooks, R. C. Beaumont, J. J. Deyoung, 1984 .

Enhancement by prolactin of carcinogen induced mammary cancerigenesis in the male rat.

C. Brooks, C. Welsch, D. Fox, 1975, British Journal of Cancer.

Reduction of Serum Prolactin in Rats by 2 Ergot Alkaloids and 2 Ergoline Derivatives: A Comparison 1

C. Brooks, C. Welsch, 1974, Proceedings of the Society for Experimental Biology and Medicine. Society for Experimental Biology and Medicine.

Theoretical approaches to solvation of biopolymers.

M Karplus, C L Brooks, M. Karplus, 1986, Methods in enzymology.

Phosphorylated variant of bovine prolactin

C. Brooks, B. Kim, Prarthana Aphale, 1990, Molecular and Cellular Endocrinology.

GH kinase activity in bovine anterior pituitary subcellular fractions

C. Brooks, J. Wicks, 1999, Endocrine.

Effects of an S84E Mutation of Bovine Growth Hormone in Transgenic Mice

C. Brooks, E. Schenck, 2006, Experimental biology and medicine.

Phosphorylation of bovine prolactin eliminates luteotropic activity in the rat.

C. Brooks, S. Saiduddin, 1998, Life sciences.

Preparative purification of phosphorylated and nonphosphorylated bovine prolactins

C. Brooks, J. Wicks, Lori A. Isaacs, 1994, Molecular and Cellular Endocrinology.

Revisiting the hexane-water interface via molecular dynamics simulations using nonadditive alkane-water potentials.

Charles L Brooks, C. Brooks, Sandeep Patel, 2006, The Journal of chemical physics.

Subdomain competition, cooperativity, and topological frustration in the folding of CheY.

Ronald D. Hills, Charles L Brooks, C. Brooks, 2008, Journal of molecular biology.

Curious structure in “canonical” alanine‐based peptides

W A Shirley, C. Brooks, W. Shirley, 1997, Proteins: Structure, Function, and Bioinformatics.

Calculating specific binding for prolactin receptor assays

C. Brooks, E. Jensen, E. Desombre, 1982, Molecular and Cellular Endocrinology.

Structure and function of a new class of human prolactin antagonists.

C. Brooks, Laura DePalatis, C. M. Almgren, 2009, Protein expression and purification.

Molecular mechanisms of prolactin and its receptor.

C. Brooks, 2012, Endocrine reviews.

Functional impact of manipulation on the relative orientation of human prolactin receptor domains.

Wei Liu, Charles L Brooks, C. Brooks, 2011, Biochemistry.

Membrane Environment Modulates the pKa Values of Transmembrane Helices

C. Brooks, Afra Panahi, 2015, The journal of physical chemistry. B.

Different elements of mini-helix 1 are required for human growth hormone or prolactin action via the prolactin receptor.

C. Brooks, F. Peterson, 2004, Protein engineering, design & selection : PEDS.

Fractionation of canine serum calcium, using a micropartition system.

C. Brooks, P. Schenck, D. Chew, 1996, American journal of veterinary research.

Failure of pH to predict ionized calcium percentage in healthy horses.

C. Brooks, C. Kohn, 1990, American journal of veterinary research.

k-Dynamics Free Energy Simulation Methods

Jennifer L. Knight, C. Brooks, JENNIFER L. KNIGHT, 2009 .

Separation of Parathyroid Hormome-Like Activity from Transforming Growth Factor-α and -β in the Canine Adenocarcinoma (CAC-8) Model of Humoral Hypercalcemia of Malignancy

C. Brooks, T. Rosol, C. Capen, 1989 .

Bone and kidney adenylate cyclase-stimulating activity produced by a hypercalcemic canine adenocarcinoma line (CAC-8) maintained in nude mice.

C. Brooks, T. Rosol, C. Capen, 1987, Cancer research.

Molecular simulations of peptide and protein unfolding: in quest of a molten globule

C. Brooks, 1993 .

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

Charles L. Brooks, Michael Feig, Michael S. Lee, 2003, J. Comput. Chem..

Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution.

M Reza Ghadiri, Charles L Brooks, C David Stout, 2006, Biochemistry.

Isolation and characterization of phosphorylated bovine prolactin.

C. Brooks, B. -. Kim, C. Brooks, 1993, The Biochemical journal.

Effect of the association time of in vivo bound prolactin on the [125I]prolactin receptor assays of female rat livers

C. Brooks, C. Welsch, 1978, Molecular and Cellular Endocrinology.

Identification of Residues Outside the Two Binding Sites That Are Critical for Activation of the Lactogenic Activity of Human Growth Hormone*

C. Brooks, K. Duda, 2003, Journal of Biological Chemistry.

Integrating folding kinetics and protein function: biphasic kinetics and dual binding specificity in a WW domain.

John Karanicolas, Charles L Brooks, J. Karanicolas, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Mechanism for ordered receptor binding by human prolactin.

Charles L Brooks, C. Brooks, U. Sivaprasad, 2004, Biochemistry.

Model-free Analysis of Protein Dynamics: Assessment of Accuracy and Model Selection Protocols Based on Molecular Dynamics Simulation

Peter E. Wright, Jianhan Chen, C. Brooks, 2004, Journal of biomolecular NMR.

How dihydrofolate reductase facilitates protonation of dihydrofolate.

Charles L Brooks, C. Brooks, T. Rod, 2003, Journal of the American Chemical Society.

Conformational change of the methionine 20 loop of Escherichia coli dihydrofolate reductase modulates pKa of the bound dihydrofolate

D. J. Price, C. Brooks, Jinhyuk Lee, 2007, Protein science : a publication of the Protein Society.

The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase

Ian F. Thorpe, C. Brooks, I. Thorpe, 2004, Proteins.

Free Gangliosides Can Alter Amyloid-β Aggregation.

Bikash R. Sahoo, C. Brooks, A. Ramamoorthy, 2022, The journal of physical chemistry letters.

Protein–drug interactions: Characterization of inhibitor binding in complexes of DHFR with trimethoprim and related derivatives

C. Brooks, Charles L. Brooks, Stephen H. Fleischmann, 1990, Proteins.

A general method to quantify quasi-equivalence in icosahedral viruses.

John E. Johnson, Charles L Brooks, Vijay S Reddy, 2002, Journal of molecular biology.

Identification and Characterization of a Regulatory Domain on the Carboxyl Terminus of the Measles Virus Nucleocapsid Protein

Charles Brooks, C. Brooks, S. Udem, 2002, Journal of Virology.

Active site dynamics in protein molecules: A stochastic boundary molecular‐dynamics approach

M. Karplus, C. Brooks, A. Brünger, 1985, Biopolymers.

Can molecular dynamics simulations provide high‐resolution refinement of protein structure?

Jianhan Chen, Charles L Brooks, C. Brooks, 2007, Proteins.

Evaluating CASP4 predictions with physical energy functions

Michael Feig, Charles L Brooks, C. Brooks, 2002, Proteins.

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

A Kolinski, J Skolnick, C L Brooks, 1999, Proteins.

Gatekeepers in the ribosomal protein s6: thermodynamics, kinetics, and folding pathways revealed by a minimalist protein model.

José N Onuchic, Charles L Brooks, J. Onuchic, 2004, Journal of molecular biology.

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

Charles L. Brooks, David A. Case, Michael Feig, 2004, J. Comput. Chem..

Thermodynamics of aqueous solvation: Solution properties of alcohols and alkanes

Charles L. Brooks, C. Brooks, Stephen H. Fleischman, 1987 .

Exploring atomistic details of pH-dependent peptide folding

Charles L Brooks, Jianhan Chen, C. Brooks, 2006, Proceedings of the National Academy of Sciences.

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

C. Brooks, M. Crowley, F. Salsbury, 2001, Proteins.

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

Charles L. Brooks, Mark A. Olson, Michael Feig, 2008, J. Comput. Chem..

The 13 Å Structure of a Chaperonin GroEL–Protein Substrate Complex by Cryo-electron Microscopy

Charles L. Brooks, Florence Tama, Mark T. Fisher, 2005 .

The species specificity of growth hormone requires the cooperative interaction of two motifs

C. Brooks, F. Peterson, 2000, FEBS letters.

Dynamics of liquid state chemical reactions: Vibrational energy relaxation of molecular iodine in liquid solution

C. Brooks, S. Adelman, M. W. Balk, 1983 .

A new classification of the amino acid side chains based on doublet acceptor energy levels.

C. Brooks, R. S. Morgan, S. Sneddon, 1988, Biophysical journal.

Helicity, circular dichroism and molecular dynamics of proteins.

C L Brooks, J D Hirst, C. Brooks, 1994, Journal of molecular biology.

Mutating aspartate in the calcium-binding site of alpha-lactalbumin: effects on the protein stability and cation binding.

C. Brooks, L. Berliner, V. Uversky, 2001, Protein engineering.

Selectivity in K+ channels is due to topological control of the permeant ion's coordinated state

David L Bostick, Charles L Brooks, C. Brooks, 2007, Proceedings of the National Academy of Sciences.

Revisiting the carboxylic acid dimers in aqueous solution: interplay of hydrogen bonding, hydrophobic interactions, and entropy.

Charles L Brooks, Harold A Scheraga, Jianhan Chen, 2008, The journal of physical chemistry. B.

Evaluation of a radioimmunoassay for type III procollagen peptide in the dog.

C. Brooks, S. Johnson, D. Dimski, 1990, Veterinary clinical pathology.

A reexamination of the hydrophobic effect: Exploring the role of the solvent model in computing the methane–methane potential of mean force

Charles L. Brooks, C. Brooks, William S. Young, 1997 .

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

Alexander D. MacKerell, Charles L. Brooks, Sandeep Patel, 2004, J. Comput. Chem..

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

C L Brooks, C. Brooks, B. Dominy, 1999, Proteins.

Assessing search strategies for flexible docking

Charles L. Brooks, Jonathan D. Hirst, Michal Vieth, 1998, J. Comput. Chem..

λ‐dynamics: A new approach to free energy calculations

Charles L. Brooks, C. Brooks, Xianjun Kong, 1996 .

Classical molecular dynamics.

D. Case, C. Brooks, E. Tajkhorshid, 2021, The Journal of chemical physics.

Role of Active Site Residues and Solvation in RNase A

M. Karplus, C. Brooks, A. Brünger, 1986 .

Molecular dynamics with internal coordinate constraints

Charles L. Brooks, Douglas J. Tobias, C. Brooks, 1988 .

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

C. Brooks, D. Tobias, 1987 .

Reproductive toxicity of butylated triphenyl phosphate and tricresyl phosphate fluids in F344 rats.

C. Brooks, C. Capen, J. Latendresse, 1994, Fundamental and applied toxicology : official journal of the Society of Toxicology.

Identifying native‐like protein structures using physics‐based potentials

Charles L. Brooks, Brian N. Dominy, C. Brooks, 2002, J. Comput. Chem..

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

Douglas J. Tobias, Charles L. Brooks, John E. Mertz, 1991 .

Implicit solvation based on generalized Born theory in different dielectric environments.

Michael Feig, Wonpil Im, Charles L Brooks, 2004, The Journal of chemical physics.

Effects of ether anesthesia on plasma prolactin sampling

C. Brooks, C. Simonel, Dr. C. W. Welsch, 1975, Experientia.

A theoretical approach to drug design. 1. Relative solvation thermodynamics for the antibacterial compound trimethoprim and ethyl derivatives substituted at the 3', 4', and 5' positions

Charles L. Brooks, C. Brooks, Stephen H. Fleischman, 1990 .

Theoretical study of blocked glycine and alanine peptide analogs

Charles L. Brooks, Michael J. Frisch, Martin Head-Gordon, 1991 .

Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units

Michael Feig, Jianhan Chen, Xiping Gong, 2019, J. Comput. Chem..

Critical importance of length-scale dependence in implicit modeling of hydrophobic interactions.

Charles L Brooks, Jianhan Chen, C. Brooks, 2007, Journal of the American Chemical Society.

Folding intermediate in the villin headpiece domain arises from disruption of a N-terminal hydrogen-bonded network.

Charles L Brooks, C. Brooks, D. Raleigh, 2007, Journal of the American Chemical Society.

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

Charles L. Brooks, Sandeep Patel, C. Brooks, 2004, J. Comput. Chem..

AB INITIO CALCULATIONS OF THE EXCITED STATES OF FORMAMIDE

C. Brooks, J. Hirst, A. D. Hirst, 1996 .

Pathogenesis of cholesteryl lipidosis of adrenocortical and ovarian interstitial cells in F344 rats caused by tricresyl phosphate and butylated triphenyl phosphate.

C. Brooks, C. Capen, J. Latendresse, 1993, Toxicology and applied pharmacology.

Exploring the space of protein folding Hamiltonians: The balance of forces in a minimalist β-barrel model

C. Brooks, J. Shea, Zhuyan Guo, 1998 .

Structure, thermodynamics, and liquid-vapor equilibrium of ethanol from molecular-dynamics simulations using nonadditive interactions.

Sandeep Patel, Charles L Brooks, C. Brooks, 2005, The Journal of chemical physics.

A nonadditive methanol force field: bulk liquid and liquid-vapor interfacial properties via molecular dynamics simulations using a fluctuating charge model.

Sandeep Patel, Charles L Brooks, C. Brooks, 2005, The Journal of chemical physics.

Biasing Potential Replica Exchange Multisite λ-Dynamics for Efficient Free Energy Calculations.

Kira A Armacost, Charles L Brooks, C. Brooks, 2015, Journal of chemical theory and computation.

Functional epitopes for site 1 of human prolactin.

C. Brooks, G. V. Rao, 2011, Biochemistry.

How to improve nature: study of the electrostatic properties of the surface of alpha-lactalbumin.

C. Brooks, L. Berliner, V. Uversky, 2005, Protein engineering, design & selection : PEDS.

Fine tuning the N-terminus of a calcium binding protein: alpha-lactalbumin.

C. Brooks, L. Berliner, V. Uversky, 1999, Proteins: Structure, Function, and Bioinformatics.

Role of the essential light chain in the activation of smooth muscle myosin by regulatory light chain phosphorylation.

C. Brooks, M. Feig, K. Taylor, 2014, Journal of structural biology.

Virus Particle Explorer (VIPER), a Website for Virus Capsid Structures and Their Computational Analyses

John E. Johnson, C L Brooks, V S Reddy, 2001, Journal of Virology.

A theoretical study of alanine dipeptide and analogs

Charles L. Brooks, Michael J. Frisch, Martin Head-Gordon, 2009 .

Ribosome motions modulate electrostatic properties

Joanna Trylska, Florence Tama, J Andrew McCammon, 2004, Biopolymers.

Calculations on folding of segment B1 of streptococcal protein G.

C L Brooks, C. Brooks, F. Sheinerman, 1998, Journal of molecular biology.

Reverse turns in blocked dipeptides are intrinsically unstable in water.

C L Brooks, C. Brooks, D. Tobias, 1990, Journal of molecular biology.

Thermodynamics of amide hydrogen bond formation in polar and apolar solvents.

C L Brooks, C. Brooks, D. Tobias, 1989, Journal of molecular biology.

Linking folding with aggregation in Alzheimer's β-amyloid peptides

Charles L Brooks, C. Brooks, Jana Khandogin, 2007, Proceedings of the National Academy of Sciences.

Hydrophobic cooperativity as a mechanism for amyloid nucleation.

Ronald D. Hills, Charles L Brooks, C. Brooks, 2007, Journal of molecular biology.

Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations.

Wonpil Im, Charles L Brooks, C. Brooks, 2007, Biophysical journal.

Topological frustration in beta alpha-repeat proteins: sequence diversity modulates the conserved folding mechanisms of alpha/beta/alpha sandwich proteins.

Ronald D. Hills, Charles L Brooks, C. Brooks, 2010, Journal of molecular biology.

Chapter 1 Molecular Simulations of pH-Mediated Biological Processes

C. Brooks, Jana Khandogin, 2007 .

Model of the toxic complex of anthrax: Responsive conformational changes in both the lethal factor and the protective antigen heptamer

Florence Tama, Charles L Brooks, C. Brooks, 2006, Protein science : a publication of the Protein Society.

Casein, actin, and tubulin expression during early involution in bovine and murine mammary tissue.

C. Brooks, C. Hodgson, D. Wiens, 1992, Journal of dairy science.

Efficient and Flexible Algorithm for Free Energy Calculations Using the λ-Dynamics Approach

Charles L. Brooks, C. Brooks, Z. Guo and, 1998 .

310 Helixes in Peptides and Proteins As Studied by Modified Zimm-Bragg Theory

C. Brooks, F. Sheinerman, 1995 .

The influence of long-range force truncation on the thermodynamics of aqueous ionic solutions

Charles L. Brooks, C. Brooks, 1987 .

Promotion of helix formation in peptides dissolved in alcohol and water-alcohol mixtures

Charles L. Brooks, Lennart Nilsson, C. Brooks, 1993 .

An abinitio study of hydrated chloride ion complexes: Evidence of polarization effects and nonadditivity

Charles L. Brooks, C. Brooks, J. B. Foresman, 1987 .

Simulations of protein folding and unfolding.

C L Brooks, C. Brooks, Charles L. Brooks, 1998, Current opinion in structural biology.

Molecular picture of folding of a small α/β protein

Charles L. Brooks, C. Brooks, F. Sheinerman, 1998 .

Chemical physics of protein folding.

J. Onuchic, P. Wolynes, M. Gruebele, 1998, Proceedings of the National Academy of Sciences of the United States of America.

Effect of gatekeepers on the early folding kinetics of a model β-barrel protein

Charles L. Brooks, José N. Onuchic, J. Onuchic, 2003 .

Tryptophan side chain electrostatic interactions determine edge-to-face vs parallel-displaced tryptophan side chain geometries in the designed beta-hairpin "trpzip2".

Olgun Guvench, Charles L Brooks, Olgun Guvench, 2005, Journal of the American Chemical Society.

Modern protein force fields behave comparably in molecular dynamics simulations

Charles L. Brooks, Daniel J. Price, C. Brooks, 2002, J. Comput. Chem..

Prediction of quaternary structure of coiled coils. Application to mutants of the GCN4 leucine zipper.

J. Skolnick, A. Kolinski, C. Brooks, 1995, Journal of molecular biology.

Erratum: New Analytic Approximation to the Standard Molecular Volume Definition and Its Application to Generalized Born Calculations (Journal of Computational Chemistry (2003) 24:11 (1348-1356))

Charles L. Brooks, Michael Feig, C. Brooks, 2003 .

Generalized Langevin theory for many‐body problems in chemical dynamics: Modelling of solid and liquid state response functions

C. Brooks, M. Berkowitz, S. Adelman, 1980 .

Methodological advances in molecular dynamics simulations of biological systems.

C L Brooks, C. Brooks, 1995, Current opinion in structural biology.

Reaction paths and free energy profiles for conformational transitions: An internal coordinate approach

Charles L. Brooks, Themis Lazaridis, Douglas J. Tobias, 1991 .

Deprotonation by Dehydration: The Origin of Ammonium Sensing in the AmtB Channel

Charles L. Brooks, David L. Bostick, C. Brooks, 2006, PLoS Comput. Biol..

Conformational flexibility in free energy simulations

C. Brooks, D. Tobias, S. Fleischman, 1989 .

Thermodynamic calculations on biological molecules

C. Brooks, 1988 .

The thermodynamics of solvophobic effects: A molecular‐dynamics study of n‐butane in carbon tetrachloride and water

Charles L. Brooks, Douglas J. Tobias, C. Brooks, 1990 .

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

Trilce Estrada, Charles L. Brooks, Michela Taufer, 2011, J. Chem. Inf. Model..

Dynamics of liquid state chemical reactions: Photolysis of molecular iodine in liquid xenon

C. Brooks, S. Adelman, 1984 .

A CHARMM analysis of the conformations of the metastasis-inhibiting laminin pentapeptide

C. Brooks, M. Mokotoff, D. R. Mckelvey, 1991, Journal of protein chemistry.

Cluster structure determination using Gaussian density distribution global minimization methods

C. Brooks, Chiachin Tsoo, 1994 .

The solution conformations of ferrichrome and deferriferrichrome determined by 1H‐nmr spectroscopy and computational modeling

C. Brooks, K. Constantine, M. Llinás, 1990, Biopolymers.

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

Charles L. Brooks, Jianhan Chen, Wonpil Im, 2005, J. Comput. Chem..

Helix−Coil Kinetics: Folding Time Scales for Helical Peptides from a Sequential Kinetic Model

Charles L. Brooks, C. Brooks, 1996 .

Homogeneous redundancy: a technique to ensure integrity of molecular simulation results using public computing

David P. Anderson, Charles L. Brooks, Michela Taufer, 2005, 19th IEEE International Parallel and Distributed Processing Symposium.

Henri Casanova

Andrew A. Chien, Henri Casanova, Charles L. Brooks, 2022 .

Temperature-dependent behavior of protein-chromophore interactions: a theoretical study of a blue fluorescent antibody.

C. Brooks, F. Salsbury, W. Han, 2003, Chemphyschem : a European journal of chemical physics and physical chemistry.

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

D. Case, C. Brooks, W. Im, 2004, J. Comput. Chem..

Thermodynamics of ionic solvation: Monte Carlo simulations of aqueous chloride and bromide ions

Charles L. Brooks, C. Brooks, 1986 .

Statistical determinants of selective ionic complexation: ions in solvent, transport proteins, and other "hosts".

C. Brooks, D. Bostick, 2009, Biophysical journal.

Reproductive Toxicity of Butylated Triphenyl Phosphate and Tricresyl Phosphate Fluids in F344 Rats

C. Brooks, C. Capen, J. Latendresse, 1994 .

Conformational equilibrium in the alanine dipeptide in the gas phase and aqueous solution : a comparison of theoretical results

Charles L. Brooks, Douglas J. Tobias, C. Brooks, 1992 .

Virtual rigid body dynamics

C. Brooks, Teresa Head‐Cordon, Charles L. Brooks, 1991, Biopolymers.

Generalized Langevin theory for many-body problems in chemical dynamics: Gas-surface collisions, vibrational energy relaxation in solids, and recombination reactions in liquids

C. Brooks, M. Berkowitz, S. Adelman, 1980 .

Dynamics of liquid state chemical reactions: Modeling of R‐dependent correlation functions

C. Brooks, S. Adelman, 1982 .

Calcium and Calmodulin-Dependent Phosphorylation of κ-Casein by a Bovine Mammary Casein Kinase

C. Brooks, 1987 .

The effect of placenta on lactogen receptor in pseudopregnant rabbits.

C. Brooks, G. Littleton, F. Grissom, 1990, Endocrine research.

The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: Lessons for protein design?

John Karanicolas, Charles L Brooks, J. Karanicolas, 2003, Proceedings of the National Academy of Sciences of the United States of America.

FoldGPCR: Structure prediction protocol for the transmembrane domain of G protein‐coupled receptors from class A

R. Stevens, C. Brooks, Jianhan Chen, 2010, Proteins.

The high dielectric constant of staphylococcal nuclease is encoded in its structural architecture.

C. Brooks, Garrett B. Goh, B. García‐Moreno E., 2011, Journal of the American Chemical Society.

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

John Karanicolas, Charles L Brooks, J. Karanicolas, 2003, Proteins.

Efficient Sampling of Ligand Orientations and Conformations in Free Energy Calculations Using the λ-Dynamics Method

Charles L. Brooks, Shinichi Banba, C. Brooks, 2000 .

An evolution of minimalist models for protein folding: from the behavior of protein-like polymers to protein function

J. Karanicolas, C. Brooks, 2004 .

Dielectric Continuum Models for Hydration Effects on Peptide Conformational Transitions

Charles L. Brooks, David A. Case, Donald Bashford, 1996 .

Study of a highly accurate and fast protein–ligand docking method based on molecular dynamics

Andrew A. Chien, Charles L. Brooks, Daniel J. Price, 2005, Concurr. Comput. Pract. Exp..

Metrics for effective resource management in global computing environments

David P. Anderson, Patricia J. Teller, Charles L. Brooks, 2005, First International Conference on e-Science and Grid Computing (e-Science'05).