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Charles Brooks

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TOP 3
Evgenia N Nikolova; Charles L Brooks; Garrett B Goh; Hashim M Al-Hashimi
Characterizing the protonation state of Cytosine in transient g·c Hoogsteen base pairs in duplex DNA.
Sean M Law; Bin W Zhang; Charles L Brooks
pH-sensitive residues in the p19 RNA silencing suppressor protein from carnation Italian ringspot virus affect siRNA binding stability.
Jennifer L Knight; Joseph D Yesselman; Charles L Brooks
Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes.

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All Publications

2013: Evgenia N Nikolova; Charles L Brooks; Garrett B Goh; Hashim M Al-Hashimi
Characterizing the protonation state of Cytosine in transient g·c Hoogsteen base pairs in duplex DNA.
Journal of the American Chemical Society 2013;135(18):6766-9.
2013: Sean M Law; Bin W Zhang; Charles L Brooks
pH-sensitive residues in the p19 RNA silencing suppressor protein from carnation Italian ringspot virus affect siRNA binding stability.
Protein science : a publication of the Protein Society 2013;22(5):595-604.
2013: Jennifer L Knight; Joseph D Yesselman; Charles L Brooks
Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes.
Journal of computational chemistry 2013;34(11):893-903.
2013: Harish Vashisth; georgios skiniotis; Charles L Brooks
Enhanced sampling and overfitting analyses in structural refinement of nucleic acids into electron microscopy maps.
The journal of physical chemistry. B 2013;117(14):3738-46.
2013: Linda Foit; Jenny S George; Bin W Zhang; Charles L Brooks; James C A Bardwell
Chaperone activation by unfolding.
Proceedings of the National Academy of Sciences of the United States of America 2013;110(14):E1254-62.
2013: Alex Dickson; Charles L Brooks
Native states of fast-folding proteins are kinetic traps.
Journal of the American Chemical Society 2013;135(12):4729-34.
2013: Ningkun Wang; James A Wells; Charles L Brooks; Jessica K Gagnon; Taylor K Johnson; Chinmay Y Majmudar; Jennifer Meagher; William C Pomerantz; Jack D Sadowsky; Jeanne A Stuckey; Anna K Mapp
Ordering a dynamic protein via a small-molecule stabilizer.
Journal of the American Chemical Society 2013;135(9):3363-6.
2013: Shanshan Cheng; Charles L Brooks
Viral capsid proteins are segregated in structural fold space.
PLoS computational biology 2013;9(2):e1002905.
2012: Catherine D Eichhorn; Jun Feng; Krishna C Suddala; Nils G Walter; Charles L Brooks; Hashim M Al-Hashimi
Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch.
Nucleic acids research 2012;40(3):1345-55.
2012: Ranjan V Mannige; Charles L Brooks; Eugene I Shakhnovich
A universal trend among proteomes indicates an oily last common ancestor.
PLoS computational biology 2012;8(12):e1002839.
2010: Mayako Michino; Jianhan Chen; Raymond C Stevens; Charles L Brooks
FoldGPCR: structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A.
Proteins 2010;78(10):2189-201.
2010: Jörg Zimmermann; Floyd E Romesberg; Charles L Brooks; Ian F Thorpe
Molecular description of flexibility in an antibody combining site.
The journal of physical chemistry. B 2010;114(21):7359-70.
2010: Ronald D Hills; Sagar V Kathuria; Louise A Wallace; Iain J Day; Charles L Brooks; C Robert Matthews
Topological frustration in beta alpha-repeat proteins: sequence diversity modulates the conserved folding mechanisms of alpha/beta/alpha sandwich proteins.
Journal of molecular biology 2010;398(2):332-50.
2009: Mayako Michino; Charles L Brooks
Predicting structurally conserved contacts for homologous proteins using sequence conservation filters.
Proteins 2009;77(2):448-53.
2009: Mayako Michino; Enrique Abola; Charles L Brooks; J Scott Dixon; John Moult; Raymond C Stevens
Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008.
Nature reviews. Drug discovery 2009;8(6):455-63.
2009: Ranjan V Mannige; Charles L Brooks
Geometric considerations in virus capsid size specificity, auxiliary requirements, and buckling.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(21):8531-6.
2009: Ronald D Hills; Charles L Brooks
Insights from coarse-grained gō models for protein folding and dynamics.
International journal of molecular sciences 2009;10(3):889-905.
2008: Mauricio Carrillo-Tripp; Charles L Brooks; Vijay S Reddy
A novel method to map and compare protein-protein interactions in spherical viral capsids.
Proteins 2008;73(3):644-55.
2008: Ronald D Hills; Charles L Brooks
Coevolution of function and the folding landscape: correlation with density of native contacts.
Biophysical journal 2008;95(9):L57-9.
2008: Ronald D Hills; Charles L Brooks
Subdomain competition, cooperativity, and topological frustration in the folding of CheY.
Journal of molecular biology 2008;382(2):485-95.
2008: Ranjan V Mannige; Charles L Brooks
Tilable nature of virus capsids and the role of topological constraints in natural capsid design.
Physical review. E, Statistical, nonlinear, and soft matter physics 2008;77(5 Pt 1):051902.
2008: Lintao Bu; Charles L Brooks
De novo prediction of the structures of M. tuberculosis membrane proteins.
Journal of the American Chemical Society 2008;130(16):5384-5.
2008: Hendrik Szurmant; Lintao Bu; Charles L Brooks; James A Hoch
An essential sensor histidine kinase controlled by transmembrane helix interactions with its auxiliary proteins.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(15):5891-6.
2008: Mark A Olson; Michael Feig; Charles L Brooks
Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions.
Journal of computational chemistry 2008;29(5):820-31.
2008: Jianhan Chen; Charles L Brooks; Jana Khandogin
Recent advances in implicit solvent-based methods for biomolecular simulations.
Current opinion in structural biology 2008;18(2):140-8.
2008: Lintao Bu; Mayako Michino; Romain M Wolf; Charles L Brooks
Improved model building and assessment of the Calcium-sensing receptor transmembrane domain.
Proteins 2008;71(1):215-26.
2008: Jianhan Chen; Charles L Brooks; Harold A Scheraga
Revisiting the carboxylic acid dimers in aqueous solution: interplay of hydrogen bonding, hydrophobic interactions, and entropy.
The journal of physical chemistry. B 2008;112(2):242-9.
2007: karunesh arora; Charles L Brooks
Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(47):18496-501.
2007: Jana Khandogin; Charles L Brooks
Linking folding with aggregation in Alzheimer's beta-amyloid peptides.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(43):16880-5.
2007: David L Bostick; Charles L Brooks
On the equivalence point for ammonium (de)protonation during its transport through the AmtB channel.
Biophysical journal 2007;92(12):L103-5.
2007: Ilja V Khavrutskii; Daniel J Price; Jinhyuk Lee; Charles L Brooks
Conformational change of the methionine 20 loop of Escherichia coli dihydrofolate reductase modulates pKa of the bound dihydrofolate.
Protein science : a publication of the Protein Society 2007;16(6):1087-100.
2007: Jianhan Chen; Charles L Brooks
Can molecular dynamics simulations provide high-resolution refinement of protein structure?
Proteins 2007;67(4):922-30.
2007: David L Bostick; Charles L Brooks
Selectivity in K+ channels is due to topological control of the permeant ion's coordinated state.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(22):9260-5.
2007: Ian F Thorpe; Charles L Brooks
Molecular evolution of affinity and flexibility in the immune system.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(21):8821-6.
2007: Ronald D Hills; Charles L Brooks
Hydrophobic cooperativity as a mechanism for amyloid nucleation.
Journal of molecular biology 2007;368(3):894-901.
2007: Jana Khandogin; Daniel P Raleigh; Charles L Brooks
Folding intermediate in the villin headpiece domain arises from disruption of a N-terminal hydrogen-bonded network.
Journal of the American Chemical Society 2007;129(11):3056-7.
2007: Jianhan Chen; Charles L Brooks
Critical importance of length-scale dependence in implicit modeling of hydrophobic interactions.
Journal of the American Chemical Society 2007;129(9):2444-5.
2007: David L Bostick; Charles L Brooks
Deprotonation by dehydration: the origin of ammonium sensing in the AmtB channel.
PLoS computational biology 2007;3(2):e22.
2007: Lintao Bu; Wonpil Im; Charles L Brooks
Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations.
Biophysical journal 2007;92(3):854-63.
2006: Jana Khandogin; Jianhan Chen; Charles L Brooks
Exploring atomistic details of pH-dependent peptide folding.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(49):18546-50.
2006: Ilja V Khavrutskii; karunesh arora; Charles L Brooks
Harmonic Fourier beads method for studying rare events on rugged energy surfaces.
The Journal of chemical physics 2006;125(17):174108.
2006: Michael B Sherman; Richard H Guenther; Florence Tama; Tim L Sit; Charles L Brooks; Albert M Mikhailov; Elena V Orlova; Timothy S Baker; Steven A Lommel
Removal of divalent cations induces structural transitions in red clover necrotic mosaic virus, revealing a potential mechanism for RNA release.
Journal of virology 2006;80(21):10395-406.
2006: Jörg Zimmermann; Erin L Oakman; Ian F Thorpe; Xinghua Shi; Paul Abbyad; Charles L Brooks; Steven G Boxer; Floyd E Romesberg
Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(37):13722-7.
2006: Florence Tama; Gang Ren; Charles L Brooks; Alok K Mitra
Model of the toxic complex of anthrax: responsive conformational changes in both the lethal factor and the protective antigen heptamer.
Protein science : a publication of the Protein Society 2006;15(9):2190-200.
2006: Jana Khandogin; Charles L Brooks
Toward the accurate first-principles prediction of ionization equilibria in proteins.
Biochemistry 2006;45(31):9363-73.
2006: Robert Konecny; Joanna Trylska; Florence Tama; Deqiang Zhang; Nathan A Baker; Charles L Brooks; J Andrew McCammon
Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids.
Biopolymers 2006;82(2):106-20.
2006: Sandeep A Patel; Charles L Brooks
Revisiting the hexane-water interface via molecular dynamics simulations using nonadditive alkane-water potentials.
The Journal of chemical physics 2006;124(20):204706.
2006: Ilja V Khavrutskii; Richard H Byrd; Charles L Brooks
A line integral reaction path approximation for large systems via nonlinear constrained optimization: application to alanine dipeptide and the beta hairpin of protein G.
The Journal of chemical physics 2006;124(19):194903.
2006: Maneesh K Yadav; Luke J Leman; Daniel J Price; Charles L Brooks; C David Stout; M Reza Ghadiri
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.
Biochemistry 2006;45(14):4463-73.
2006: Jianhan Chen; Wonpil Im; Charles L Brooks
Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field.
Journal of the American Chemical Society 2006;128(11):3728-36.
2006: Florence Tama; Charles L Brooks
Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.
Annual review of biophysics and biomolecular structure 2006;35():115-33.
2006: Craig M Shepherd; Ian A Borelli; Gabriel C Lander; Padmaja Natarajan; Vinay Siddavanahalli; Chandrajit Bajaj; John E Johnson; Charles L Brooks; Vijay S Reddy
VIPERdb: a relational database for structural virology.
Nucleic acids research 2006;34(Database issue):D386-9.
2005: Jianhan Chen; Wonpil Im; Charles L Brooks
Application of torsion angle molecular dynamics for efficient sampling of protein conformations.
Journal of computational chemistry 2005;26(15):1565-78.
2005: Kakoli Mitra; Christiane Schaffitzel; Tanvir Shaikh; Florence Tama; Simon Jenni; Charles L Brooks; Nenad Ban; Joachim Frank
Structure of the E. coli protein-conducting channel bound to a translating ribosome.
Nature 2005;438(7066):318-24.
2005: Daniel J Price; Charles L Brooks
Detailed considerations for a balanced and broadly applicable force field: a study of substituted benzenes modeled with OPLS-AA.
Journal of computational chemistry 2005;26(14):1529-41.
2005: Sandeep Patel; Charles L Brooks
Structure, thermodynamics, and liquid-vapor equilibrium of ethanol from molecular-dynamics simulations using nonadditive interactions.
The Journal of chemical physics 2005;123(16):164502.
2005: Padmaja Natarajan; Gabriel C Lander; Craig M Shepherd; Vijay S Reddy; Charles L Brooks; John E Johnson
Exploring icosahedral virus structures with VIPER.
Nature reviews. Microbiology 2005;3(10):809-17.
2005: Ian F Thorpe; Charles L Brooks
Conformational substates modulate hydride transfer in dihydrofolate reductase.
Journal of the American Chemical Society 2005;127(37):12997-3006.
2005: Jana Khandogin; Charles L Brooks
Constant pH molecular dynamics with proton tautomerism.
Biophysical journal 2005;89(1):141-57.
2005: Wonpil Im; Charles L Brooks
Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(19):6771-6.
2005: Scott Falke; Florence Tama; Charles L Brooks; Edward P Gogol; Mark T Fisher
The 13 angstroms structure of a chaperonin GroEL-protein substrate complex by cryo-electron microscopy.
Journal of molecular biology 2005;348(1):219-30.
2005: Olgun Guvench; Charles L Brooks
Tryptophan side chain electrostatic interactions determine edge-to-face vs parallel-displaced tryptophan side chain geometries in the designed beta-hairpin "trpzip2".
Journal of the American Chemical Society 2005;127(13):4668-74.
2005: Olgun Guvench; Daniel J Price; Charles L Brooks
Receptor rigidity and ligand mobility in trypsin-ligand complexes.
Proteins 2005;58(2):407-17.
2005: Florence Tama; Michael Feig; Jun Liu; Charles L Brooks; Kenneth A Taylor
The requirement for mechanical coupling between head and S2 domains in smooth muscle myosin ATPase regulation and its implications for dimeric motor function.
Journal of molecular biology 2005;345(4):837-54.
2005: Florence Tama; Charles L Brooks
Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis.
Journal of molecular biology 2005;345(2):299-314.
2005: Sandeep Patel; Charles L Brooks
A nonadditive methanol force field: bulk liquid and liquid-vapor interfacial properties via molecular dynamics simulations using a fluctuating charge model.
The Journal of chemical physics 2005;122(2):024508.
2005: Wonpil Im; Jianhan Chen; Charles L Brooks
Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models.
Advances in protein chemistry 2005;72():173-98.
2005: Jianhan Chen; Hyung-Sik Won; Wonpil Im; H Jane Dyson; Charles L Brooks
Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling.
Journal of biomolecular NMR 2005;31(1):59-64.
2004: Jianhan Chen; Wonpil Im; Charles L Brooks
Refinement of NMR structures using implicit solvent and advanced sampling techniques.
Journal of the American Chemical Society 2004;126(49):16038-47.
2004: Daniel J Price; Charles L Brooks
A modified TIP3P water potential for simulation with Ewald summation.
The Journal of chemical physics 2004;121(20):10096-103.
2004: Ian F Thorpe; Charles L Brooks
The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase.
Proteins 2004;57(3):444-57.
2004: Florence Tama; Osamu Miyashita; Charles L Brooks
Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM.
Journal of structural biology 2004;147(3):315-26.
2004: Michael S Lee; Freddie Salsbury; Charles L Brooks
Constant-pH molecular dynamics using continuous titration coordinates.
Proteins 2004;56(4):738-52.
2004: Sandeep Patel; Alexander D. Mackerell; Charles L Brooks
CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.
Journal of computational chemistry 2004;25(12):1504-14.
2004: Joanna Trylska; Robert Konecny; Florence Tama; Charles L Brooks; J Andrew McCammon
Ribosome motions modulate electrostatic properties.
Biopolymers 2004;74(6):423-31.
2004: Antitsa D Stoycheva; Charles L Brooks; José N Onuchic
Gatekeepers in the ribosomal protein s6: thermodynamics, kinetics, and folding pathways revealed by a minimalist protein model.
Journal of molecular biology 2004;340(3):571-85.
2004: Jianhan Chen; Charles L Brooks; Peter Wright
Model-free analysis of protein dynamics: assessment of accuracy and model selection protocols based on molecular dynamics simulation.
Journal of biomolecular NMR 2004;29(3):243-57.
2004: Philippe Ferrara; Holger Gohlke; Daniel J Price; Gerhard Klebe; Charles L Brooks
Assessing scoring functions for protein-ligand interactions.
Journal of medicinal chemistry 2004;47(12):3032-47.
2004: Olgun Guvench; Charles L Brooks
Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations.
Journal of computational chemistry 2004;25(8):1005-14.
2004: Michael Feig; John Karanicolas; Charles L Brooks
MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.
Journal of molecular graphics & modelling 2004;22(5):377-95.
2004: Florence Tama; Osamu Miyashita; Charles L Brooks
Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis.
Journal of molecular biology 2004;337(4):985-99.
2004: Michael Feig; Charles L Brooks
Recent advances in the development and application of implicit solvent models in biomolecule simulations.
Current opinion in structural biology 2004;14(2):217-24.
2004: Wonpil Im; Charles L Brooks
De novo folding of membrane proteins: an exploration of the structure and NMR properties of the fd coat protein.
Journal of molecular biology 2004;337(3):513-9.
2004: John Karanicolas; Charles L Brooks
Integrating folding kinetics and protein function: biphasic kinetics and dual binding specificity in a WW domain.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(10):3432-7.
2004: Michael Feig; Alexey Onufriev; Michael S Lee; Wonpil Im; David A Case; Charles L Brooks
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures.
Journal of computational chemistry 2004;25(2):265-84.
2004: Sandeep Patel; Charles L Brooks
CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations.
Journal of computational chemistry 2004;25(1):1-15.
2004: Michael Feig; Wonpil Im; Charles L Brooks
Implicit solvation based on generalized Born theory in different dielectric environments.
The Journal of chemical physics 2004;120(2):903-11.
2003: Y Zenmei Ohkubo; Charles L Brooks
Exploring Flory's isolated-pair hypothesis: statistical mechanics of helix-coil transitions in polyalanine and the C-peptide from RNase A.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(24):13916-21.
2003: John Karanicolas; Charles L Brooks
Improved Gō-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions.
Journal of molecular biology 2003;334(2):309-25.
2003: John Karanicolas; Charles L Brooks
The importance of explicit chain representation in protein folding models: an examination of Ising-like models.
Proteins 2003;53(3):740-7.
2003: Wonpil Im; Michael S Lee; Charles L Brooks
Generalized born model with a simple smoothing function.
Journal of computational chemistry 2003;24(14):1691-702.
2003: Badry D Bursulaya; Maxim Totrov; Ruben Abagyan; Charles L Brooks
Comparative study of several algorithms for flexible ligand docking.
Journal of computer-aided molecular design 2003;17(11):755-63.
2003: Wonpil Im; Michael Feig; Charles L Brooks
An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins.
Biophysical journal 2003;85(5):2900-18.
2003: Freddie Salsbury; Wen-Ge Han; Louis Noodleman; Charles L Brooks
Temperature-dependent behavior of protein-chromophore interactions: a theoretical study of a blue fluorescent antibody.
Chemphyschem : a European journal of chemical physics and physical chemistry 2003;4(8):848-55.
2003: Florence Tama; Mikel Valle; Joachim Frank; Charles L Brooks
Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(16):9319-23.
2003: Michael S Lee; Michael Feig; Freddie Salsbury; Charles L Brooks
New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.
Journal of computational chemistry 2003;24(11):1348-56.
2003: Thomas H Rod; Jennifer L Radkiewicz; Charles L Brooks
Correlated motion and the effect of distal mutations in dihydrofolate reductase.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(12):6980-5.
2003: John Karanicolas; Charles L Brooks
The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: lessons for protein design?
Proceedings of the National Academy of Sciences of the United States of America 2003;100(7):3954-9.
2002: Joan-Emma Shea; José N Onuchic; Charles L Brooks
Probing the folding free energy landscape of the Src-SH3 protein domain.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(25):16064-8.
2002: K V Damodaran; Vijay S Reddy; John E Johnson; Charles L Brooks
A general method to quantify quasi-equivalence in icosahedral viruses.
Journal of molecular biology 2002;324(4):723-37.
2002: Michael Feig; Charles L Brooks
Evaluating CASP4 predictions with physical energy functions.
Proteins 2002;49(2):232-45.
2002: John Karanicolas; Charles L Brooks
The origins of asymmetry in the folding transition states of protein L and protein G.
Protein science : a publication of the Protein Society 2002;11(10):2351-61.
2002: Florence Tama; Willy Wriggers; Charles L Brooks
Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory.
Journal of molecular biology 2002;321(2):297-305.
2002: Daniel J Price; Charles L Brooks
Modern protein force fields behave comparably in molecular dynamics simulations.
Journal of computational chemistry 2002;23(11):1045-57.
2002: Charles L Brooks
Protein and peptide folding explored with molecular simulations.
Accounts of chemical research 2002;35(6):447-54.
2002: Brian Dominy; Dieter Perl; Franz X Schmid; Charles L Brooks
The effects of ionic strength on protein stability: the cold shock protein family.
Journal of molecular biology 2002;319(2):541-54.
2002: Florence Tama; Charles L Brooks
The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus.
Journal of molecular biology 2002;318(3):733-47.
2002: Charles L Brooks
Viewing protein folding from many perspectives.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(3):1099-100.
2002: Brian Dominy; Charles L Brooks
Identifying native-like protein structures using physics-based potentials.
Journal of computational chemistry 2002;23(1):147-60.
2001: Vijay S Reddy; Padmaja Natarajan; B Okerberg; K Li; K V Damodaran; R T Morton; Charles L Brooks; John E Johnson
Virus Particle Explorer (VIPER), a website for virus capsid structures and their computational analyses.
Journal of virology 2001;75(24):11943-7.
2001: O Roche; R Kiyama; Charles L Brooks
Ligand-protein database: linking protein-ligand complex structures to binding data.
Journal of medicinal chemistry 2001;44(22):3592-8.
2001: Freddie Salsbury; M F Crowley; Charles L Brooks
Modeling of the metallo-beta-lactamase from B. fragilis: structural and dynamic effects of inhibitor binding.
Proteins 2001;44(4):448-59.
2001: Charles L Brooks; José N Onuchic; D J Wales
Statistical thermodynamics. Taking a walk on a landscape.
Science (New York, N.Y.) 2001;293(5530):612-3.
2000: Michael Feig; Piotr Rotkiewicz; Andrzej Kolinski; Jeffrey Skolnick; Charles L Brooks
Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models.
Proteins 2000;41(1):86-97.
1999: J E Shea; José N Onuchic; Charles L Brooks
Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(22):12512-7.
1999: Brian Dominy; Charles L Brooks
Methodology for protein-ligand binding studies: application to a model for drug resistance, the HIV/FIV protease system.
Proteins 1999;36(3):318-31.
1999: DEBASISA MOHANTY; Brian Dominy; Andrzej Kolinski; Charles L Brooks; Jeffrey Skolnick
Correlation between knowledge-based and detailed atomic potentials: application to the unfolding of the GCN4 leucine zipper.
Proteins 1999;35(4):447-52.
1998: M Vieth; J D Hirst; Charles L Brooks
Do active site conformations of small ligands correspond to low free-energy solution structures?
Journal of computer-aided molecular design 1998;12(6):563-72.
1998: Charles L Brooks; Martin Gruebele; José N Onuchic; P G Wolynes
Chemical physics of protein folding.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(19):11037-8.
1998: FB Sheinerman; Charles L Brooks
Calculations on folding of segment B1 of streptococcal protein G.
Journal of molecular biology 1998;278(2):439-56.
1998: Charles L Brooks
Simulations of protein folding and unfolding.
Current opinion in structural biology 1998;8(2):222-6.
1998: FB Sheinerman; Charles L Brooks
Molecular picture of folding of a small alpha/beta protein.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(4):1562-7.
1998: Vijay S Reddy; H A Giesing; R T Morton; A Kumar; C B Post; Charles L Brooks; John E Johnson
Energetics of quasiequivalence: computational analysis of protein-protein interactions in icosahedral viruses.
Biophysical journal 1998;74(1):546-58.
1997: Z Guo; Charles L Brooks
Thermodynamics of protein folding: a statistical mechanical study of a small all-beta protein.
Biopolymers 1997;42(7):745-57.
1997: FB Sheinerman; Charles L Brooks
A molecular dynamics simulation study of segment B1 of protein G.
Proteins 1997;29(2):193-202.
1997: Z Guo; Charles L Brooks; E M Boczko
Exploring the folding free energy surface of a three-helix bundle protein.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(19):10161-6.
1997: W A Shirley; Charles L Brooks
Curious structure in "canonical" alanine-based peptides.
Proteins 1997;28(1):59-71.
1996: J D Hirst; M Vieth; Jeffrey Skolnick; Charles L Brooks
Predicting leucine zipper structures from sequence.
Protein engineering 1996;9(8):657-62.
1996: M Vieth; Andrzej Kolinski; Charles L Brooks; Jeffrey Skolnick
Prediction of the quaternary structure of coiled coils: GCN4 leucine zipper and its mutants.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1996;():653-62.
1995: M Vieth; Andrzej Kolinski; Charles L Brooks; Jeffrey Skolnick
Prediction of quaternary structure of coiled coils. Application to mutants of the GCN4 leucine zipper.
Journal of molecular biology 1995;251(3):448-67.
1995: E M Boczko; Charles L Brooks
First-principles calculation of the folding free energy of a three-helix bundle protein.
Science (New York, N.Y.) 1995;269(5222):393-6.
1994: M Vieth; Andrzej Kolinski; Charles L Brooks; Jeffrey Skolnick
Prediction of the folding pathways and structure of the GCN4 leucine zipper.
Journal of molecular biology 1994;237(4):361-7.