Publications for Charles L. Brooks III
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Manuscripts in Press
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247.
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RV Mannige and CL Brooks, III.
On the tilable nature of virus capsids and the role of topological constraints in natural capsid design. Phys Rev E, 2008, in the press .
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246.
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M Taufer, RS Armen, JH Chen, PJ Teller and CL Brooks, III.
Computational Multi-Scale Modeling in Protein-Ligand Docking. IEEE Engineering in Medicine and Biology, 2008, in the press .
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Journal Articles
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245.
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L Bu and CL Brooks, III.
De novo prediction of the structures of M. tuberculosis membrane proteins. J Am Chem Soc, 2008, 130 (16), 5384-5. PubMed
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244.
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L Bu, M Michino, RM Wolf and CL Brooks, III.
Improved model building and assessment of the Calcium-sensing receptor transmembrane domain. Proteins, 2008, 71 (1), 215-26. PubMed
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243.
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J Chen and CL Brooks, III.
Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions. Phys Chem Chem Phys, 2008, 10 (4), 471-81. PubMed
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242.
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J Chen, CL Brooks, III and J Khandogin.
Recent advances in implicit solvent-based methods for biomolecular simulations. Curr Opin Struct Biol, 2008, 18, 140-148. PubMed
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241.
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J Chen, CL Brooks, III and HA Scheraga.
Revisiting the carboxylic Acid dimers in aqueous solution: interplay of hydrogen bonding, hydrophobic interactions, and entropy. J Phys Chem B, 2008, 112 (2), 242-9. PubMed
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240.
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J Lee, J Chen, CL Brooks, III and W Im.
Application of solid-state NMR restraint potentials in membrane protein modeling. J Magn Reson, 2008, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18462966 .
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239.
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MA Olson, M Feig and CL Brooks, III.
Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions. J Comput Chem, 2008, 29 (5), 820-31. PubMed
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238.
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H Szurmant, L Bu, CL Brooks, III and JA Hoch.
An essential sensor histidine kinase controlled by transmembrane helix interactions with its auxiliary proteins. Proc Natl Acad Sci, USA, 2008, 105 (15), 5891-6. PubMed
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237.
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L Zhong, JF Matthews, MJ Crowley, T Rignall, C Talon, JM Cleary, RC Walker, G Chukkapalli, C McCabe, MR Nimlos, CL Brooks, III, ME Himmel and JW Brady.
Interactions of the Complete Cellobiohydrolast I from Trichodera reesei with Microcrystalline Cellulose Ib. Cellulose, 2008, 15, 261-273 .
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Manuscripts in Press
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236.
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M Tripp, CL Brooks, III and VS Reddy.
A novel method to map and compare protein-protein interactions in spherical viral capsids. Proteins, 2007, in the press .
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Journal Articles
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235.
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K Arora and CL Brooks, III.
Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism. Proc Natl Acad Sci, USA, 2007, 104 (47), 18496-501. PubMed
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234.
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DL Bostick and CL Brooks, III.
Deprotonation by Dehydration: The Origin of Ammonium Sensing in the AmtB Channel. PLoS Comput Biol, 2007, 3 (2), e22. PubMed
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233.
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DL Bostick and CL Brooks, III.
Selectivity in K+ channels is due to topological control of the permeant ion's coordinated state. Proc Natl Acad Sci, USA, 2007, 104 (22), 9260-5. PubMed
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232.
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DL Bostick and CL Brooks, III.
On the Equivalence Point for Ammonium (De)protonation during Its Transport through the AmtB Channel. Biophys J, 2007, 92 (12), L103-5. PubMed
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231.
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L Bu, W Im and CL Brooks, III.
Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations. Biophys J, 2007, 92 (3), 854-63. PubMed
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230.
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J Chen and CL Brooks, III.
Critical importance of length-scale dependence in implicit modeling of hydrophobic interactions. J Am Chem Soc, 2007, 129 (9), 2444-5. PubMed
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229.
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J Chen and CL Brooks, III.
Can molecular dynamics simulations provide high-resolution refinement of protein structure. Proteins, 2007, 67 (4), 922-30. PubMed
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228.
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RD Hills, Jr. and CL Brooks, III.
Hydrophobic cooperativity as a mechanism for amyloid nucleation. J Mol Biol, 2007, 368 (3), 894-901. PubMed
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227.
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J Khandogin and CL Brooks, III.
Linking folding with aggregation in Alzheimer's beta-amyloid peptides. Proc Natl Acad Sci, USA, 2007, 104 (43), 16880-16885. PubMed
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226.
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J Khandogin, DP Raleigh and CL Brooks, III.
Folding intermediate in the villin headpiece domain arises from disruption of a N-terminal hydrogen-bonded network. J Am Chem Soc, 2007, 129 (11), 3056-7. PubMed
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225.
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IV Khavrutskii, DJ Price, J Lee and CL Brooks, III.
Conformational change of the methionine 20 loop of Escherichia coli dihydrofolate reductase modulates pKa of the bound dihydrofolate. Protein Sci, 2007, 16 (6), 1087-100. PubMed
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224.
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HD Nguyen, VS Reddy and CL Brooks, III.
Deciphering the kinetic mechanism of spontaneous self-assembly of icosahedral capsids. Nano Lett, 2007, 7 (2), 338-44. PubMed
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223.
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M Taufer, A Kerstens, T Estrada, DA Flores, R Zamudio, PJ Teller, RS Armen and CL Brooks, III.
Moving Volunteer Computing towards Knowledge-Constructed, Dynamically-Adaptive Modeling and Scheduling. IDPDS, 2007, 1-8 .
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222.
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IF Thorpe and CL Brooks, III.
Molecular evolution of affinity and flexibility in the immune system. Proc Natl Acad Sci, USA, 2007, 104 (21), 8821-6. PubMed
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Book Chapters
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221.
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J Khandogin and CL Brooks, III.
Molecular Simulations of pH-Mediated Biological Processes. Annual Reports in Computational Chemistry, 2007, D Spellmeyer andR Wheeler, Elsevier, New York, NY, Pgs 1-xx.
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Journal Articles
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220.
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J Chen, W Im and CL Brooks, III.
Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field. J Am Chem Soc, 2006, 128 (11), 3728-36. PubMed
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219.
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J Khandogin and CL Brooks, III.
Toward the accurate first-principles prediction of ionization equilibria in proteins. Biochemistry, 2006, 45 (31), 9363-73. PubMed
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218.
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J Khandogin, J Chen and CL Brooks, III.
Exploring atomistic details of pH-dependent peptide folding. Proc Natl Acad Sci, USA, 2006, 103 (49), 18546-50. PubMed
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217.
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IV Khavrutskii, K Arora and CL Brooks, III.
Harmonic Fourier beads method for studying rare events on rugged energy surfaces. J Chem Phys, 2006, 125 (17), -.
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216.
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IV Khavrutskii, RH Byrd and CL Brooks, III.
A line integral reaction path approximation for large systems via nonlinear constrained optimization: Application to alanine dipeptide and the beta hairpin of protein G. J Chem Phys, 2006, 124 (19), -.
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215.
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R Konecny, J Trylska, F Tama, D Zhang, NA Baker, CL Brooks, III and JA McCammon.
Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers, 2006, 82 (2), 106-20. PubMed
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214.
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S Patel and CL Brooks, III.
Fluctuating charge force fields: Recent developments and applications from small molecules to macromolecular biological systems. Molec Simul, 2006, 32 (3-4), 231-249.
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213.
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SA Patel and CL Brooks, III.
Revisiting the hexane-water interface via molecular dynamics simulations using nonadditive alkane-water potentials. J Chem Phys, 2006, 124 (20), 204706. PubMed
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212.
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CM Shepherd, IA Borelli, G Lander, P Natarajan, V Siddavanahalli, C Bajaj, JE Johnson, CL Brooks, III and VS Reddy.
VIPERdb: a relational database for structural virology. Nucleic Acids Res, 2006, 34 (Database issue), D386-9. PubMed
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211.
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MB Sherman, RH Guenther, F Tama, TL Sit, CL Brooks, III, AM Mikhailov, EV Orlova, TS Baker and SA Lommel.
Removal of divalent cations induces structural transitions in red clover necrotic mosaic virus, revealing a potential mechanism for RNA release. J Virol, 2006, 80 (21), 10395-406. PubMed
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210.
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F Tama and CL Brooks, III.
SYMMETRY, FORM, AND SHAPE: Guiding Principles for Robustness in Macromolecular Machines. Annu Rev Biophys Biomol Struct, 2006, 35, 115-33. PubMed
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209.
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F Tama, G Ren, CL Brooks, III and AK Mitra.
Model of the toxic complex of anthrax: Responsive conformational changes in both the lethal factor and the protective antigen heptamer. Protein Sci, 2006, 15 (9), 2190-200. PubMed
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208.
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M Taufer, C An, A Kerstens and CL Brooks, III.
Predictor@Home: A Protein Structure Prediction Supercomputer Based on Global Computing. IEEE Trans Parallel and Distributed Computing, 2006, 17, 786-96 .
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207.
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MK Yadav, LJ Leman, DJ Price, CL Brooks, III, CD Stout and MR 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. PubMed
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206.
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J Zimmermann, EL Oakman, IF Thorpe, X Shi, P Abbyad, CL Brooks, III, SG Boxer and FE Romesberg.
Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics. Proc Natl Acad Sci, USA, 2006, 103 (37), 13722-7. PubMed
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Book Chapters
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205.
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F Tama and CL Brooks, III.
Unveiling molecular mechanisms of biological functions in large macromolecular assemblies using elastic network normal mode analysis. Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems, 2006, Q Cui andI Bahar, Chapman & Hall/CRC, Pgs 112-136.
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Journal Articles
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204.
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CL Brooks, III.
Editorial. J Comput Chem, 2005, 26 (16), 1667. PubMed
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203.
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J Chen, W Im and CL Brooks, III.
Application of torsion angle molecular dynamics for efficient sampling of protein conformations. J Comput Chem, 2005, 26 (15), 1565-78. PubMed
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202.
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J Chen, HS Won, W Im, HJ Dyson and CL Brooks, III.
Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling. J Biomol NMR, 2005, 31 (1), 59-64. PubMed
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201.
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S Falke, F Tama, CL Brooks, III, EP Gogol and MT Fisher.
The 13 Å structure of a chaperonin GroEL-protein substrate complex by cryo-electron microscopy. J Mol Biol, 2005, 348 (1), 219-30. PubMed
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200.
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O Guvench and CL Brooks, III.
Tryptophan side chain electrostatic interactions determine edge-to-face vs parallel-displaced tryptophan side chain geometries in the designed beta-hairpin "trpzip2". J Am Chem Soc, 2005, 127 (13), 4668-74. PubMed
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199.
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O Guvench, DJ Price and CL Brooks, III.
Receptor rigidity and ligand mobility in trypsin-ligand complexes. Proteins, 2005, 58 (2), 407-17. PubMed
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198.
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W Im and CL Brooks, III.
Chemical Theory and Computation Special Feature: Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations. Proc Natl Acad Sci, USA, 2005, 102 (19), 6771-6. PubMed
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197.
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W Im, J Chen and CL Brooks, III.
Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models. Adv Protein Chem, 2005, 72, 173-98. PubMed
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196.
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J Khandogin and CL Brooks, III.
Constant pH Molecular Dynamics with Proton Tautomerism. Biophys J, 2005, 89 (1), 141-57. PubMed
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195.
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K Mitra, C Schaffitzel, T Shaikh, F Tama, S Jenni, CL Brooks, III, N Ban and J Frank.
Structure of the E. coli protein-conducting channel bound to a translating ribosome. Nature, 2005, 438 (7066), 318-24. PubMed
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194.
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P Natarajan, GC Lander, CM Shepherd, VS Reddy, CL Brooks, III and JE Johnson.
Exploring icosahedral virus structures with VIPER. Nat Rev Microbiol, 2005, 3 (10), 809-17. PubMed
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193.
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S Patel and CL Brooks, III.
A nonadditive methanol force field: Bulk liquid and liquid-vapor interfacial properties via molecular dynamics simulations using a fluctuating charge model. J Chem Phys, 2005, 122 (2), 24508. PubMed
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192.
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S Patel and CL Brooks, III.
Structure, thermodynamics, and liquid-vapor equilibrium of ethanol from molecular-dynamics simulations using nonadditive interactions. J Chem Phys, 2005, 123 (16), 164502. PubMed
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191.
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DJ Price and CL Brooks, III.
Detailed considerations for a balanced and broadly applicable force field: a study of substituted benzenes modeled with OPLS-AA. J Comput Chem, 2005, 26 (14), 1529-41. PubMed
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190.
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F Tama and CL Brooks, III.
Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis. J Mol Biol, 2005, 345 (2), 299-314. PubMed
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189.
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F Tama, M Feig, J Liu, CL Brooks, III and KA Taylor.
The Requirement for Mechanical Coupling Between Head and S2 Domains in Smooth Muscle Myosin ATPase Regulation and its Implications for Dimeric Motor Function. J Mol Biol, 2005, 345 (4), 837-854. PubMed
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188.
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M Taufer, M Crowley, D Price, A Chien and CL Brooks, III.
Study of an Accurate and Fast Protein-Ligand Docking Algorithm based on Molecular Dynamics. Concurrency and Computation: Practice and Experience, 2005, 17, 1627-41 .
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187.
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IF Thorpe and CL Brooks, III.
Conformational substates modulate hydride transfer in dihydrofolate reductase. J Am Chem Soc, 2005, 127 (37), 12997-3006. PubMed
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186.
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J Trylska, JA McCammon and CL Brooks, III.
Exploring assembly energetics of the 30S ribosomal subunit using an implicit solvent approach. J Am Chem Soc, 2005, 127 (31), 11125-33. PubMed
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Conference Proceedings
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185.
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M Taufer, C An, A Kerstens and CL Brooks, III.
Predictor@Home: A "Protein Structure Prediction Supercomputer" Based on Public-Resource Computing. Proceedings of the 4th IEEE International Workshop on High Performance Computational Biology (HiCOMB 2005), 2005, Denver, Colorado.
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184.
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M Taufer, D Anderson, P Cicotti and CL Brooks, III.
Homogeneous Redundancy: a Technique to Ensure Integrity of Molecular Simulation Results Using Public Computing. Proceedings of 14th Heterogeneous Computing Workshop (HCW 2005), 2005, Denver, Colorado.
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183.
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M Taufer, PJ Teller, DP Anderson and CL Brooks, III.
Metrics for Effective Resource Management in Global Computing Environmentsst. Proceedings of the 1st IEEE International Conference on e-Science and Grid Technologies (eScience 2005), 2005, Melbourne, Australia.
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Journal Articles
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182.
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J Chen, CL Brooks, III and PE Wright.
Model-free analysis of protein dynamics: assessment of accuracy and model selection protocols based on molecular dynamics simulation. J Biomol NMR, 2004, 29 (3), 243-57. PubMed
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181.
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J Chen, W Im and CL Brooks, III.
Refinement of NMR structures using implicit solvent and advanced sampling techniques. J Am Chem Soc, 2004, 126 (49), 16038-47. PubMed
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180.
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BN Dominy, H Minoux and CL Brooks, III.
An electrostatic basis for the stability of thermophilic proteins. Proteins, 2004, 57 (1), 128-41. PubMed
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179.
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M Feig and CL Brooks, III.
Recent advances in the development and application of implicit solvent models in biomolecule simulations. Curr Opin Struct Biol, 2004, 14 (2), 217-24. PubMed
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178.
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M Feig, W Im and CL Brooks, III.
Implicit solvation based on generalized Born theory in different dielectric environments. J Chem Phys, 2004, 120 (2), 903-11. PubMed
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177.
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M Feig, J Karanicolas and CL Brooks, III.
MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. J Mol Graph Model, 2004, 22 (5), 377-95. PubMed
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176.
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M Feig, A Onufriev, MS Lee, W Im, DA Case and CL Brooks, III.
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. J Comput Chem, 2004, 25 (2), 265-84. PubMed
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175.
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P Ferrara, H Gohlke, DJ Price, G Klebe and CL Brooks, III.
Assessing scoring functions for protein-ligand interactions. J Med Chem, 2004, 47 (12), 3032-47. PubMed
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174.
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O Guvench and CL Brooks, III.
Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations. J Comput Chem, 2004, 25 (8), 1005-14. PubMed
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173.
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W Im and CL Brooks, III.
De novo folding of membrane proteins: an exploration of the structure and NMR properties of the fd coat protein. J Mol Biol, 2004, 337 (3), 513-9. PubMed
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172.
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J Karanicolas and CL Brooks, III.
An evolution of minimalist models for protein folding: from the behavior of protein-like polymers to protein function. Biosilico, 2004, 2 (3), 127-133 .
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171.
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J Karanicolas and CL Brooks, III.
Integrating folding kinetics and protein function: Biphasic kinetics and dual binding specificity in a WW domain. Proc Natl Acad Sci, USA, 2004, 101 (10), 3432-7. PubMed
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170.
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MS Lee, FR Salsbury, Jr. and CL Brooks, III.
Constant-pH molecular dynamics using continuous titration coordinates. Proteins, 2004, 56 (4), 738-52. PubMed
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169.
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AD Mackerell, Jr., M Feig and CL Brooks, III.
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, 25 (11), 1400-15. PubMed
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168.
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AD MacKerell, Jr., M Feig and CL Brooks, III.
Improved treatment of the protein backbone in empirical force fields. J Am Chem Soc, 2004, 126 (3), 698-9. PubMed
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167.
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A Natrajan, M Crowley, N Wilkins-Diehr, MA Humphrey, AD Fox, AS Grimshaw and CL Brooks, III.
Studying protein folding on the Grid: experiences using CHARMM on NPACI resources under Legion. Concurrency and Computation: Practice and Experience, 2004, 16, 385-397 .
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166.
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S Patel and CL Brooks, III.
CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations. J Comput Chem, 2004, 25 (1), 1-15. PubMed
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165.
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S Patel, AD Mackerell, Jr. and CL Brooks, III.
CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. J Comput Chem, 2004, 25 (12), 1504-14. PubMed
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164.
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DJ Price and CL Brooks, III.
A modified TIP3P water potential for simulation with Ewald summation. J Chem Phys, 2004, 121 (20), 10096-103. PubMed
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163.
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AD Stoycheva, CL Brooks, III and JN Onuchic.
Gatekeepers in the ribosomal protein S6: thermodynamics, kinetics, and folding pathways revealed by a minimalist protein model. J Mol Biol, 2004, 340 (3), 571-85. PubMed
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162.
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F Tama, O Miyashita and CL Brooks, III.
Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. J Mol Biol, 2004, 337 (4), 985-99. PubMed
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161.
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F Tama, O Miyashita and CL Brooks, III.
Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. J Struct Biol, 2004, 147 (3), 315-26. PubMed
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160.
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IF Thorpe and CL Brooks, III.
The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase. Proteins, 2004, 57 (3), 444-57. PubMed
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159.
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J Trylska, R Konecny, F Tama, CL Brooks, III and JA McCammon.
Ribosome motions modulate electrostatic properties. Biopolymers, 2004, 74 (6), 423-31. PubMed
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Book Chapters
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158.
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VS Reddy, P Natarajan, G Lander, C Qu, CL Brooks, III and JE Johnson.
Virus Particle Explorer (VIPER): A repository of virus capsid structures. Conformational proteomics of macromolecular Architecture, 2004, RH Cheng andL Hammer, World Scientific Pub Co., Singapore, Pgs 403-412.
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Conference Proceedings
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157.
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D Kondo, M Taufer, CL Brooks, III, H Casanova and A Chien.
Characterizing and Evaluating Desktop Grids: An Empirical Study. Proceedings of IPDPS 2004, IEEE/ACM International Parallel and Distributed Processing Symposium, 2004, Santa Fe, New Mexico.
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156.
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M Taufer, M Crowley, D Price, A Chien and CL Brooks, III.
Study of an Accurate and Fast Protein-Ligand Docking Algorithm based on Molecular Dynamics. Proceedings of the 3rd IEEE International Workshop on High Performance Computational Biology (HiCOMB 2004), 2004, Santa Fe, New Mexico..
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Journal Articles
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155.
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CL Brooks and DA Case.
Theory and simulation - The control and timescale of structure and reactivity in biological systems: from peptide folding to cellular networks - Editorial overview. Curr Opin Struct Biol, 2003, 13 (2), 143-145 .
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154.
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BD Bursulaya, M Totrov, R Abagyan and CL Brooks, III.
Comparative study of several algorithms for flexible ligand docking. J Comput Aided Mol Des, 2003, 17 (11), 755-63. PubMed
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153.
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M Feig, AD MacKerell, Jr. and CL Brooks, III.
Force Field Influence on the Observation of.pi.-Helical Protein Structures in Molecular Dynamics Simulations. J Phys Chem B, 2003, 107 (12), 2831-2836 .
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152.
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W Im, M Feig and CL Brooks, III.
An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. Biophys J, 2003, 85 (5), 2900-18. PubMed
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151.
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W Im, MS Lee and CL Brooks, III.
Generalized born model with a simple smoothing function. J Comput Chem, 2003, 24 (14), 1691-702. PubMed
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150.
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J Karanicolas and CL Brooks, III.
The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: lessons for protein design. Proc Natl Acad Sci, USA, 2003, 100 (7), 3954-9. PubMed
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149.
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J Karanicolas and CL Brooks, III.
Improved Go-like Models Demonstrate the Robustness of Protein Folding Mechanisms Towards Non-native Interactions. J Mol Biol, 2003, 334 (2), 309-25. PubMed
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148.
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J Karanicolas and CL Brooks, III.
The importance of explicit chain representation in protein folding models: an examination of Ising-like models. Proteins, 2003, 53 (3), 740-7. PubMed
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147.
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MS Lee, M Feig, FR Salsbury, Jr. and CL Brooks, III.
New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations. J Comput Chem, 2003, 24 (11), 1348-56. PubMed
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146.
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YZ Ohkubo and CL Brooks, III.
Exploring Flory's isolated-pair hypothesis: statistical mechanics of helix-coil transitions in polyalanine and the C-peptide from RNase A. Proc Natl Acad Sci, USA, 2003, 100 (24), 13916-21. PubMed
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145.
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TH Rod and CL Brooks, III.
How dihydrofolate reductase facilitates protonation of dihydrofolate. J Am Chem Soc, 2003, 125 (29), 8718-9. PubMed
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144.
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TH Rod, JL Radkiewicz and CL Brooks, III.
Correlated motion and the effect of distal mutations in dihydrofolate reductase. Proc Natl Acad Sci, USA, 2003, 100 (12), 6980-5. PubMed
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143.
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FR Salsbury, Jr., WG Han, L Noodleman and CL Brooks, III.
Temperature-dependent behavior of protein-chromophore interactions: a theoretical study of a blue fluorescent antibody. Chemphyschem, 2003, 4 (8), 848-55. PubMed
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142.
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A Stoycheva, JN Onuchic and CL Brooks, III.
Effects of gatekeepers on the early folding kinetics of a model b-barrel protein. J Chem Phys, 2003, 119 (11), 5722-5729 .
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141.
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F Tama, M Valle, J Frank and CL Brooks, III.
Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc Natl Acad Sci, USA, 2003, 100 (16), 9319-23. PubMed
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140.
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IF Thorpe and CL Brooks, III.
Barriers to hydride transfer in wild type and mutant dihydrofolate reductase from E-coli. J Phys Chem B, 2003, 107 (50), 14042-14051 .
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139.
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G Wu, DH Robertson, CL Brooks, III and M Vieth.
Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm. J Comput Chem, 2003, 24 (13), 1549-62. PubMed
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Journal Articles
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138.
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CL Brooks, III.
Viewing protein folding from many perspectives. Proc Natl Acad Sci, USA, 2002, 99 (3), 1099-100. PubMed
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137.
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CL Brooks, III.
Protein and peptide folding explored with molecular simulations. Acc Chem Res, 2002, 35 (6), 447-54. PubMed
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136.
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CL Brooks, III.
Protein folding: with a little help. Nature, 2002, 420 (6911), 33-4. PubMed
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135.
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KV Damodaran, VS Reddy, JE Johnson and CL Brooks, III.
A general method to quantify quasi-equivalence in icosahedral viruses. J Mol Biol, 2002, 324 (4), 723-37. PubMed
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134.
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BN Dominy and CL Brooks, III.
Identifying native-like protein structures using physics-based potentials. J Comput Chem, 2002, 23 (1), 147-60. PubMed
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133.
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BN Dominy, D Perl, FX Schmid and CL Brooks, III.
The effects of ionic strength on protein stability: the cold shock protein family. J Mol Biol, 2002, 319 (2), 541-54. PubMed
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132.
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M Feig and CL Brooks, III.
Evaluating CASP4 predictions with physical energy functions. Proteins, 2002, 49 (2), 232-45. PubMed
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131.
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A Fiser, M Feig, CL Brooks, III and A Sali.
Evolution and physics in comparative protein structure modeling. Acc Chem Res, 2002, 35 (6), 413-21. PubMed
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130.
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J Karanicolas and CL Brooks, III.
The origins of asymmetry in the folding transition states of protein L and protein G. Protein Sci, 2002, 11 (10), 2351-61. PubMed
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129.
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MS Lee, FR Salsbury, Jr. and CL Brooks, III.
Novel generalized Born methods. J Chem Phys, 2002, 116 (24), 10606-10614 .
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128.
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DJ Price and CL Brooks, III.
Modern protein force fields behave comparably in molecular dynamics simulations. J Comput Chem, 2002, 23 (11), 1045-57. PubMed
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127.
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JE Shea, JN Onuchic and CL Brooks, III.
Probing the folding free energy landscape of the Src-SH3 protein domain. Proc Natl Acad Sci, USA, 2002, 99 (25), 16064-8. PubMed
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126.
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F Tama and CL Brooks, III.
The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus. J Mol Biol, 2002, 318 (3), 733-47. PubMed
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125.
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F Tama, W Wriggers and CL Brooks, III.
Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. J Mol Biol, 2002, 321 (2), 297-305. PubMed
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Journal Articles
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124.
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CL Brooks, III, JN Onuchic and DJ Wales.
Perspectives: statistical thermodynamics. Taking a walk on a landscape. Science, 2001, 293 (5530), 612-613 .
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123.
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KV Damodaran, S Banba and CL Brooks, III.
Application of Multiple Topology l-Dynamics to a Host-Guest System: b-Cyclodextrin with Substituted Benzenes. J Phys Chem B, 2001, 105 (38), 9316-9322 .
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122.
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VS Reddy, P Natarajan, B Okerberg, K Li, KV Damodaran, RT Morton, CL Brooks, III and JE Johnson.
Virus Particle Explorer (VIPER), a website for virus capsid structures and their computational analyses. J Virol, 2001, 75 (24), 11943-7. PubMed
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121.
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O Roche, R Kiyama and CL Brooks, III.
Ligand-protein database: linking protein-ligand complex structures to binding data. J Med Chem, 2001, 44 (22), 3592-8. PubMed
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120.
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FR Salsbury, Jr., MF Crowley and CL Brooks, III.
Modeling of the metallo-beta-lactamase from B. fragilis: structural and dynamic effects of inhibitor binding. Proteins, 2001, 44 (4), 448-59. PubMed
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119.
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KA Sharp and CL Brooks, III.
Theory and simulation: Old wine in new bottles. Curr Opin Struct Biol, 2001, 11 (2), 209-211 .
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Book Chapters
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118.
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S Banba, Z Guo and CL Brooks, III.
New free energy based methods for ligand binding from detailed structure-function to multiple-ligand screening. Free Energy Calculations in Rational Drug Design, 2001, MR Reddy andMD Erion, Kluwar Academic/Plenum Publishers, New York, Pgs 195-223.
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117.
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JE Shea and CL Brooks, III.
From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding. Annu Rev Phys Chem, 2001, HL Strauss, Annual Reviews, Palo Alto, Pgs 499-535. PubMed
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Journal Articles
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116.
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S Banba and CL Brooks, III.
Free energy screening of small ligands binding to an artificial protein cavity. J Chem Phys, 2000, 113 (8), 3423-3433 .
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115.
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S Banba, Z Guo and CL Brooks, III.
Efficient Sampling of Ligand Orientations and Conformations in Free Energy Calculations Using the l-Dynamics Method. J Phys Chem B, 2000, 104 (29), 6903-6910 .
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114.
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BD Bursulaya and CL Brooks, III.
Comparative Study of the Folding Free Energy Landscape of a Three-Stranded b-Sheet Protein with Explicit and Implicit Solvent Models. J Phys Chem B, 2000, 104 (51), 12378-12383 .
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113.
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M Feig, P Rotkiewicz, A Kolinski, J Skolnick and CL Brooks, III.
Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models. Proteins, 2000, 41 (1), 86-97. PubMed
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112.
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JL Radkiewicz and CL Brooks, III.
Protein Dynamics in Enzymatic Catalysis: Exploration of Dihydrofolate Reductase. J Am Chem Soc, 2000, 122 (2), 225-231 .
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111.
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J-E Shea, JN Onuchic and CL Brooks, III.
Energetic frustration and the nature of the transition state in protein folding. J Chem Phys, 2000, 113 (17), 7663-7671 .
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110.
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A Van der Vaart, BD Bursulaya, CL Brooks, III and KM Merz, Jr..
Are Many-Body Effects Important in Protein Folding. J Phys Chem B, 2000, 104 (40), 9554-9563 .
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Journal Articles
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109.
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BD Bursulaya and CL Brooks, III.
Folding free energy surface of a three-stranded b-sheet protein. J Am Chem Soc, 1999, 121 (43), 9947-9951 .
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108.
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BN Dominy and CL Brooks, III.
Development of a Generalized Born Model Parametrization for Proteins and Nucleic Acids. J Phys Chem B, 1999, 103 (18), 3765-3773 .
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107.
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BN Dominy and CL Brooks, III.
Methodology for protein-ligand binding studies: application to a model for drug resistance, the HIV/FIV protease system. Proteins, 1999, 36 (3), 318-31. PubMed
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106.
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D Mohanty, BN Dominy, A Kolinski, CL Brooks, III and J Skolnick.
Correlation between knowledge-based and detailed atomic potentials: application to the unfolding of the GCN4 leucine zipper. Proteins, 1999, 35 (4), 447-52. PubMed
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105.
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JE Shea, JN Onuchic and CL Brooks, III.
Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A. Proc Natl Acad Sci, USA, 1999, 96 (22), 12512-7. PubMed
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Book Chapters
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104.
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JD Hirst, B Dominy, Z Guo, M Vieth and CL Brooks, III.
Conformational and energetic aspects of receptor-ligand recognition. Rational Drug Design, 1999, Pgs 12-36.
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Journal Articles
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103.
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CL Brooks, III.
Simulations of protein folding and unfolding. Curr Opin Struct Biol, 1998, 8 (2), 222-6. PubMed
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102.
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CL Brooks, III, M Gruebele, JN Onuchic and PG Wolynes.
Chemical physics of protein folding. Proc Natl Acad Sci, USA, 1998, 95 (19), 11037-8. PubMed
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101.
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Z Guo and CL Brooks, III.
Rapid screening of binding affinities: Application of the l-dynamics method to a trypsin-inhibitor system. J Am Chem Soc, 1998, 120 (8), 1920-1921 .
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100.
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Z Guo, CL Brooks, III and X Kong.
Efficient and Flexible Algorithm for Free Energy Calculations Using the l-Dynamics Approach. J Phys Chem B, 1998, 102 (11), 2032-2036 .
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99.
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VS Reddy, HA Giesing, RT Morton, A Kumar, CB Post, CL Brooks, III and JE Johnson.
Energetics of quasiequivalence: computational analysis of protein-protein interactions in icosahedral viruses. Biophys J, 1998, 74 (1), 546-58. PubMed
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98.
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J-E Shea, YD Nochomovitz, Z Guo and CL Brooks, III.
Exploring the space of protein folding Hamiltonians: The balance of forces in a minimalist b-barrel model. J Chem Phys, 1998, 109 (7), 2895-2903 .
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97.
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FB Sheinerman and CL Brooks, III.
Molecular picture of folding of a small alpha/beta protein. Proc Natl Acad Sci, USA, 1998, 95 (4), 1562-7. PubMed
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96.
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FB Sheinerman and CL Brooks, III.
Calculations on folding of segment B1 of streptococcal protein G. J Mol Biol, 1998, 278 (2), 439-56. PubMed
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95.
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M Vieth, JD Hirst and CL Brooks, III.
Do active site conformations of small ligands correspond to low free-energy solution structures. J Comput Aided Mol Des, 1998, 12 (6), 563-72. PubMed
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94.
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M Vieth, JD Hirst, BN Dominy, H Daigler and CL Brooks, III.
Assessing search strategies for flexible docking. J Comp Chem, 1998, 19 (14), 1623-1631 .
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93.
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M Vieth, JD Hirst, A Kolinski and CL Brooks, III.
Assessing energy functions for flexible docking. J Comp Chem, 1998, 19 (14), 1612-1622 .
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Book Chapters
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92.
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AD MacKerell, Jr., BR Brooks, CL Brooks, III, L Nilsson, B Roux, Y Won and M Karplus.
CHARMM: The energy function and its parameterization. Encyclopedia of Computational Chemistry, 1998, PvR Schleyer, NL Allinger, T Clark, J Gasteiger, PA Kollman, HF Schaefer, III andPR Schreiner, John Wiley & Sons, Ltd., Chichester, UK, Pgs 271-277.
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Journal Articles
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91.
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Z Guo and CL Brooks, III.
Thermodynamics of protein folding: a statistical mechanical study of a small all-beta protein. Biopolymers, 1997, 42 (7), 745-57. PubMed
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90.
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Z Guo, CL Brooks, III and EM Boczko.
Exploring the folding free energy surface of a three-helix bundle protein. Proc Natl Acad Sci, USA, 1997, 94 (19), 10161-6. PubMed
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89.
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JD Hirst, DM Hirst and CL Brooks, III.
Multireference Configuration Interaction Calculations of Electronic States of N-Methylformamide, Acetamide, and N-Methylacetamide. J Phys Chem A, 1997, 101 (26), 4821-4827 .
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88.
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FB Sheinerman and CL Brooks, III.
A molecular dynamics simulation study of segment B1 of protein G. Proteins, 1997, 29 (2), 193-202. PubMed
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87.
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WA Shirley and CL Brooks, III.
Curious structure in "canonical" alanine-based peptides. Proteins, 1997, 28 (1), 59-71. PubMed
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86.
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WS Young and CL Brooks, III.
A reexamination of the hydrophobic effect: Exploring the role of the solvent model in computing the methane-methane potential of mean force. J Chem Phys, 1997, 106 (22), 9265-9269 .
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Journal Articles
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85.
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CL Brooks, III.
Helix-Coil Kinetics: Folding Time Scales for Helical Peptides from a Sequential Kinetic Model. J Phys Chem, 1996, 100 (7), 2546-9 .
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84.
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CL Brooks, III, CB Post and P Rossky.
Biography of Martin Karplus. J Phys Chem, 1996, 100 (7), 2458 .
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83.
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JD Hirst, DM Hirst and CL Brooks, III.
Ab Initio Calculations of the Excited States of Formamide. J Phys Chem, 1996, 100 (32), 13487-13491 .
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82.
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JD Hirst, M Vieth, J Skolnick and CL Brooks, III.
Predicting leucine zipper structures from sequence. Protein Eng, 1996, 9 (8), 657-62. PubMed
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81.
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ME Karpen and CL Brooks, III.
Modeling protein conformation by molecular mechanics and dynamics. Prot Struct Pred, 1996, 229-261 .
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80.
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X Kong and CL Brooks, III.
l-Dynamics: a new approach to free energy calculations. J Chem Phys, 1996, 105 (6), 2314-2423 .
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79.
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K Oesapay, WS Young, D Bashford, CL Brooks, III and DA Case.
Dielectric Continuum Models for Hydration Effects on Peptide Conformational Transitions. J Phys Chem, 1996, 100 (7), 2698-705 .
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78.
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T Simonson and CL Brooks, III.
Charge Screening and the Dielectric Constant of Proteins: Insights from Molecular Dynamics. J Am Chem Soc, 1996, 118 (35), 8452-8458 .
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77.
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M Vieth, A Kolinski, CL Brooks, III and J Skolnick.
A Hierarchical Approach to the Prediction of Quaternary Structure of GCN4 and its Mutants. DIMACS, 1996, 23, 233-236 .
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76.
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M Vieth, A Kolinski, CL Brooks, III and J Skolnick.
Prediction of the quaternary structure of coiled coils: GCN4 leucine zipper and its mutants. Pac Symp Biocomput, 1996, 653-62, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9390265 .
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75.
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WS Young and CL Brooks, III.
A microscopic view of helix propagation: N and C-terminal helix growth in alanine helices. J Mol Biol, 1996, 259 (3), 560-72. PubMed
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Journal Articles
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74.
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EM Boczko and CL Brooks, III.
First-principles calculation of the folding free energy of a three-helix bundle protein. Science, 1995, 269 (5222), 393-6. PubMed
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73.
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CL Brooks, III.
Methodological advances in molecular dynamics simulations of biological systems. Curr Opin Struct Biol, 1995, 5 (2), 211-5. PubMed
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72.
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JD Hirst and CL Brooks, III.
Molecular dynamics simulations of isolated helices of myoglobin. Biochemistry, 1995, 34 (23), 7614-21. PubMed
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71.
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FB Sheinerman and CL Brooks, III.
310 Helices in Peptides and Proteins As Studied by Modified Zimm-Bragg Theory. J Am Chem Soc, 1995, 117 (40), 10098-103 .
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70.
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M Vieth, A Kolinski, CL Brooks, III and J Skolnick.
Prediction of quaternary structure of coiled coils. Application to mutants of the GCN4 leucine zipper. J Mol Biol, 1995, 251 (3), 448-67. PubMed
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69.
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WS Young and CL Brooks, III.
Dynamic load balancing algorithms for replicated data molecular dynamics. J Comp Chem, 1995, 16 (6), 715-22 .
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Book Chapters
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68.
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J Skolnick, M Vieth, A Kolinski and CL Brooks, III.
De novo simulations of the folding of GCN4 and its mutants. Jerusalem Symposia on Quantum Chemistry and Biochemistry, 1995, A Pullman, et al., Kluwar Academic Publishers, Netherlands, Pgs 95-8.
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Journal Articles
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67.
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JD Hirst and CL Brooks, III.
Helicity, circular dichroism and molecular dynamics of proteins. J Mol Biol, 1994, 243 (2), 173-8. PubMed
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66.
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C Tsoo and CL Brooks, III.
Cluster Structure Determination Using Gaussian Density Annealing. J Chem Phys, 1994, 101, 6405-6411 .
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65.
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M Vieth, A Kolinski, CL Brooks, III and J Skolnick.
Prediction of the folding pathways and structure of the GCN4 leucine zipper. J Mol Biol, 1994, 237 (4), 361-7. PubMed
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64.
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WS Young and CL Brooks, III.
Implementation of a data parallel, logical domain decomposition method for interparticle interactions in molecular dynamics of structured molecular fluids. J Comp Chem, 1994, 15 (1), 44-53 .
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Journal Articles
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63.
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EM Boczko and CL Brooks, III.
Constant-temperature free energy surfaces for physical and chemical processes. J Phys Chem, 1993, 97 (17), 4509-13 .
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62.
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C Brooks, III and DA Case.
Simulations of peptide conformational dynamics and thermodynamics. Chem Rev, 1993, 93 (7), 2487-502 .
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61.
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CL Brooks, III.
Molecular simulations of peptide and protein unfolding: In quest of a molten globule. Curr Opin Struct Biol, 1993, 3 (1), 92-8 .
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60.
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CL Brooks, III and L Nilsson.
Promotion of helix formation in peptides dissolved in alcohol and water-alcohol mixtures. J Am Chem Soc, 1993, 115 (23), 11034-5 .
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59.
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ME Karpen, DJ Tobias and CL Brooks, III.
Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV. Biochemistry, 1993, 32 (2), 412-20. PubMed
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58.
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J Skolnick, A Kolinski, CL Brooks, III, A Godzik and A Rey.
A method for predicting protein structure from sequence. Curr Biol, 1993, 3 (7), 414-23 .
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57.
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SF Sneddon and CL Brooks, III.
Protein motions: structural and functional aspects. Mol Struct Biol, 1993, 114-63 .
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Journal Articles
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56.
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CL Brooks, III.
Characterization of "native" apomyoglobin by molecular dynamics simulation. J Mol Biol, 1992, 227 (2), 375-80. PubMed
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55.
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JJ McDonald and CL Brooks, III.
A theoretical approach to drug design. 3. Relative thermodynamics of inhibitor binding by E. coli dihydrofolate reductase to ethyl derivatives of trimethoprim substituted at the 3', 4', and 5' positions. J Am Chem Soc, 1992, 114 (6), 2062-72 .
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54.
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SF Sneddon and CL Brooks, III.
The conformations of proline-linked donor-acceptor systems. J Am Chem Soc, 1992, 114 (21), 8220-5 .
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53.
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DJ Tobias and CL Brooks, III.
Conformational equilibrium in the alanine dipeptide in the gas phase and aqueous solution: a comparison of theoretical results. J Phys Chem, 1992, 96 (9), 3864-70 .
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52.
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DJ Tobias, SF Sneddon and CL Brooks, III.
Stability of a model beta-sheet in water. J Mol Biol, 1992, 227 (4), 1244-52. PubMed
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Journal Articles
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51.
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CL Brooks, III, WS Young and DJ Tobias.
Molecular Simulations on Supercomputers. Intl J Supercomput Appl, 1991, 5, 98-112 .
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50.
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T Head-Gordon and CL Brooks, III.
Virtual rigid body dynamics. Biopolymers, 1991, 31 (1), 77-100. PubMed
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49.
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T Head-Gordon, M Head-Gordon, MJ Frisch, CL Brooks, III and JA Pople.
Theoretical study of blocked glycine and alanine peptide analogs. J Am Chem Soc, 1991, 113 (16), 5989-97 .
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48.
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T Lazaridis, DJ Tobias, CL Brooks, III and ME Paulaitis.
Reaction paths and free energy profiles for conformational transitions: An internal coordinate approach. J Chem Phys, 1991, 95, 7612-7625 .
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47.
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JJ McDonald and CL Brooks, III.
Theoretical approach to drug design. 2. Relative thermodynamics of inhibitor binding by chicken dihydrofolate reductase to ethyl derivatives of trimethoprim substituted at 3'-, 4'-, and 5'-positions. J Am Chem Soc, 1991, 113 (6), 2295-301 .
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46.
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DR McKelvey, CL Brooks and M Mokotoff.
A CHARMM analysis of the conformations of the metastasis-inhibiting laminin pentapeptide. J Protein Chem, 1991, 10 (3), 265-71. PubMed
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45.
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JE Mertz, DJ Tobias, CL Brooks, III and UC Singh.
Vector and parallel algorithms for the molecular dynamics simulation of macromolecules on shared-memory computers. J Comp Chem, 1991, 12 (10), 1270-7 .
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44.
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DJ Tobias and CL Brooks, III.
Thermodynamics and mechanism of alpha helix initiation in alanine and valine peptides. Biochemistry, 1991, 30 (24), 6059-70. PubMed
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43.
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DJ Tobias, JE Mertz and CL Brooks, III.
Nanosecond time scale folding dynamics of a pentapeptide in water. Biochemistry, 1991, 30 (24), 6054-8. PubMed
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Book Chapters
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42.
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CL Brooks, III.
Semiclassical methods for large molecules of biological importance. Theor Models Chem Bonding, 1991, Springer-Verlag, Pgs 51-64.
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41.
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SF Sneddon and CL Brooks, III.
Protein Motions: Structural and Functional Aspects. Molecular Structures in Biology, 1991, R Diamond, Oxford University Press, Oxford, England, Pgs 113-160.
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Conference Proceedings
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40.
|
DJ Tobias, SF Sneddon and CL Brooks, III.
The stability of protein secondary structures in aqueous solution. AIP Conference Proceedings, 1991, Obernai, France.
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Journal Articles
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39.
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CL Brooks, III and SH Fleischman.
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. J Am Chem Soc, 1990, 112 (9), 3307-12 .
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38.
|
KL Constantine, A De Marco, M Madrid, CL Brooks, III and M Llinas.
The solution conformations of ferrichrome and deferriferrichrome determined by 1H-NMR spectroscopy and computational modeling. Biopolymers, 1990, 30 (3-4), 239-56. PubMed
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37.
|
SH Fleischman and CL Brooks, III.
Protein-drug interactions: characterization of inhibitor binding in complexes of DHFR with trimethoprim and related derivatives. Proteins, 1990, 7 (1), 52-61. PubMed
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36.
|
DJ Tobias and CL Brooks, III.
The thermodynamics of solvophobic effects: a molecular-dynamics study of n-butane in carbon tetrachloride and water. J Chem Phys, 1990, 92 (4), 2582-92 .
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35.
|
DJ Tobias, SF Sneddon and CL Brooks, III.
Reverse turns in blocked dipeptides are intrinsically unstable in water. J Mol Biol, 1990, 216 (3), 783-96. PubMed
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Book Chapters
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34.
|
CL Brooks, III.
Molecular simulations of protein structure, dynamics and thermodynamics. Computer Modeling of Fluids, Polymers and Solids, 1990, CRA Catlow, Bath, England, Pgs 289-334.
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Journal Articles
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33.
|
CL Brooks, III and M Karplus.
Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme. J Mol Biol, 1989, 208 (1), 159-81. PubMed
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32.
|
T Head-Gordon and CL Brooks, III.
Evaluation of simple model descriptions of the diffusional association rate for enzyme-ligand systems. J Phys Chem, 1989, 93 (1), 490-4 .
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31.
|
T Head-Gordon, M Head-Gordon, MJ Frisch, CL Brooks, III and J Pople.
A theoretical study of alanine dipeptide and analogs. Int J Quant Chem, Quant Biol Symp, 1989, 16, 311-22 .
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30.
|
SF Sneddon, RS Morgan and CL Brooks, III.
Toward a model of electronic coupling in proteins. J Phys Chem, 1989, 93 (24), 8115-18 .
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29.
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SF Sneddon, DJ Tobias and CL Brooks, III.
Thermodynamics of amide hydrogen bond formation in polar and apolar solvents. J Mol Biol, 1989, 209 (4), 817-20. PubMed
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28.
|
DJ Tobias, CL Brooks, III and SH Fleischman.
Conformational flexibility in free energy simulations. Chem Phys Lett, 1989, 156 (2-3), 256-60 .
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Journal Articles
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27.
|
SF Sneddon and CL Brooks, III.
The influence of geometrical fluctuations on electron tunneling barriers in proteins. Int J Quant Chem, Quant Biol Symp, 1988, 15, 23-32 .
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26.
|
SF Sneddon, RS Morgan and CL Brooks, III.
A new classification of the amino acid side chains based on doublet acceptor energy levels. Biophys J, 1988, 53 (1), 83-9. PubMed
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25.
|
DJ Tobias and CL Brooks, III.
Molecular dynamics with internal coordinate constraints. J Chem Phys, 1988, 89 (8), 5115-27 .
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Book Chapters
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24.
|
CL Brooks, III, M Karplus and BM Pettitt.
Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics. Advances in Chemical Physics, 1988, I Prigogine andSA Rice, John Wiley & Sons, New York, Pgs Pages.
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Conference Proceedings
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23.
|
CL Brooks, III.
Thermodynamic calculations on biological molecules. Computer Simulations of Biomolecular Systems: Theoretical and Experimental Applications, 1988, Princeton, N.J..
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Journal Articles
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22.
|
CL Brooks, III.
Scaling behavior of atomic motions: Fractal analysis of particle trajectories. Phys Rev A, 1987, 35 (12), 5178-82 .
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21.
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CL Brooks, III.
The influence of long-range force truncation on the thermodynamics of aqueous ionic solutions. J Chem Phys, 1987, 86 (9), 5156-62 .
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20.
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SH Fleischman and CL Brooks, III.
Thermodynamics of aqueous solvation: solution properties of alcohols and alkanes. J Chem Phys, 1987, 87 (5), 3029-37 .
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19.
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JB Foresman and CL Brooks, III.
An ab initio study of hydrated chloride ion complexes: evidence of polarization effects and nonadditivity. J Chem Phys, 1987, 87 (10), 5892-4 .
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18.
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T Head-Gordon and CL Brooks, III.
The role of electrostatics in the binding of small ligands to enzymes. J Phys Chem, 1987, 91 (12), 3342-9 .
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17.
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DJ Tobias and CL Brooks, III.
Calculation of free energy surfaces using the methods of thermodynamic perturbation theory. Chem Phys Lett, 1987, 142 (6), 472-6 .
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Journal Articles
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16.
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C Brooks, III, A Brunger, M Francl, K Haydock, LC Allen and M Karplus.
Role of active site residues and solvation in RNase A. Annals NY Acad Sci, 1986, 471 (Int. Symp. Bioorg. Chem., 1985), 295-8 .
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15.
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CL Brooks, III.
Thermodynamics of ionic solvation: Monte Carlo simulations of aqueous chloride and bromide ions. J Phys Chem, 1986, 90 (25), 6680-4 .
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Book Chapters
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14.
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CL Brooks, III and M Karplus.
Theoretical approaches to solvation of biopolymers. Biomembranes a volume of Methods in Enzymology, 1986, Academic Press, Inc., New York, Pgs 369-400.
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Journal Articles
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13.
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CL Brooks, III, A Brunger and M Karplus.
Active site dynamics in protein molecules: a stochastic boundary molecular-dynamics approach. Biopolymers, 1985, 24 (5), 843-65. PubMed
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12.
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CL Brooks, III, B Montgomery Pettitt and M Karplus.
Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids. J Chem Phys, 1985, 83 (11), 5897-908 .
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11.
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AT Brunger, CL Brooks, III and M Karplus.
Active site dynamics of ribonuclease. Proc Natl Acad Sci, USA, 1985, 82 (24), 8458-62. PubMed
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Journal Articles
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10.
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CL Brooks, III and SA Adelman.
Dynamics of liquid-state chemical reactions: photolysis of molecular iodine in liquid xenon. J Chem Phys, 1984, 80 (11), 5598-609 .
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9.
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A Bruenger, CL Brooks, III and M Karplus.
Stochastic boundary conditions for molecular dynamics simulations of ST2 water. Chem Phys Lett, 1984, 105 (5), 495-500 .
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8.
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C Romig, CL Brooks, III, JJ Deyoung and RC Beaumont.
Dioxygen-bridged and monomeric cobalt(III) complexes with 1,3-diamino-2-(aminomethyl)propane and ethylenediamine. Inorg Chim Acta, 1984, 86 (1), 13-18 .
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Journal Articles
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7.
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MW Balk, CL Brooks, III and SA Adelman.
Dynamics of liquid state chemical reactions: photodissociation dynamics and geminate recombination of molecular iodine in liquid solution. J Chem Phys, 1983, 79 (2), 804-15 .
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6.
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CL Brooks, III, MW Balk and SA Adelman.
Dynamics of liquid state chemical reactions: vibrational energy relaxation of molecular iodine in liquid solution. J Chem Phys, 1983, 79 (2), 784-803 .
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5.
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CL Brooks, III and M Karplus.
Deformable stochastic boundaries in molecular dynamics. J Chem Phys, 1983, 79 (12), 6312-25 .
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Journal Articles
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4.
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SA Adelman and CL Brooks, III.
Generalized Langevin models and condensed-phase chemical reaction dynamics. J Phys Chem, 1982, 86 (9), 1511-24 .
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3.
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CL Brooks, III and SA Adelman.
Dynamics of liquid state chemical reactions: modeling of R-dependent correlation functions. J Chem Phys, 1982, 77 (1), 484-97 .
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2.
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CL Brooks, III and SA Adelman.
Dynamics of liquid state chemical reactions: R-dependent correlation functions for atomic iodine + atomic iodine in carbon tetrachloride. J Chem Phys, 1982, 76 (2), 1007-23 .
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Journal Articles
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1.
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CL Brooks, III, M Berkowitz and SA Adelman.
Generalized Langevin theory for many-body problems in chemical dynamics: gas-surface collisions, vibrational energy relaxation in solids, and recombination reactions in liquids. J Chem Phys, 1980, 73 (9), 4353-64 .
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