Publications

2013

Manuscript in Press

  1. K Arora and CL Brooks III. Multiple Intermediates, Diverse Conformations, and Cooperative Conformational Changes Underlie the Catalytic Hydride Transfer Reaction of Dihydrofolate Reductase. Top Curr Chem, 2013, in the press.   PubMed
  1. L Foit, JS George, BW Zhang, CL Brooks III and JC Bardwell. Chaperone activation by unfolding. Proc Natl Acad Sci U S A, 2013, in the press.   PubMed
  1. GB Goh, JL Knight and C Brooks III. pH-dependent dynamics of complex RNA macromolecules. J Chem Theor Comp, 2013, in the press.
  1. SM Law, BW Zhang and CL Brooks III. pH-sensitive residues in the P19 RNA silencing suppressor protein from carnation italian ringspot virus affect siRNA binding stability. Protein Sci, 2013, in the press.   PubMed
  1. H Vashisth, G Skiniotis and CL Brooks III. Enhanced Sampling Assisted Structural Refinement of Nucleic Acids into Electron Microscopy Maps. J Phys Chem B, 2013, in the press.

Journal Article

  1. CL Brooks III, M Ehara, G Frenking and PR Schreiner. New paint and a new engine. J Comput Chem, 2013, 34:1.  PubMed
  1. S Cheng and CL Brooks III. Viral capsid proteins are segregated in structural fold space. PLoS Comput Biol, 2013, 9:e1002905. PMCID: 3567143.  PubMed
  1. A Dickson and CL Brooks III. Native States of fast-folding proteins are kinetic traps. J Am Chem Soc, 2013, 135:4729-34.  PubMed
  1. GB Goh, JL Knight and CL Brooks III. Towards Accurate Prediction of Protonation Equilibrium of Nucleic Acids. J Phys Chem Lett, 2013, 4:760-766. PMCID: 3601767.  PubMed
  1. JL Knight, JD Yesselman and CL Brooks III. Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes. J Comput Chem, 2013, 34:893-903.  PubMed
  1. N Wang, CY Majmudar, WC Pomerantz, JK Gagnon, JD Sadowsky, JL Meagher, TK Johnson, JA Stuckey, CL Brooks III, JA Wells and AK Mapp. Ordering a dynamic protein via a small-molecule stabilizer. J Am Chem Soc, 2013, 135:3363-6. PMCID: 3607081.  PubMed

2012

Journal Article

  1. A Dickson and CL Brooks III. Quantifying Hub-like Behavior in Protein Folding Networks. J Chem Theor Comput, 2012, 8:3044-3052.  PubMed
  1. GB Goh, JL Knight and CL Brooks III. Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent. J Chem Theor Comput, 2012, 8:36-46. PMCID: 3277849.  PubMed
  1. DM Jacobsen, ZQ Bao, P O'Brien, CL Brooks III and MA Young. Price to be paid for two-metal catalysis: magnesium ions that accelerate chemistry unavoidably limit product release from a protein kinase. J Am Chem Soc, 2012, 134:15357-70. PMCID: 3446636.  PubMed
  1. JT King, EJ Arthur, CL Brooks III and KJ Kubarych. Site-Specific Hydration Dynamics of Globular Proteins and the Role of Constrained Water in Solvent Exchange with Amphiphilic Cosolvents. J Phys Chem B, 2012, 116:5604–5611. PMCID: 3422398.  PubMed
  1. CY Majmudar, JW Hojfeldt, CJ Arevang, WC Pomerantz, JK Gagnon, PJ Schultz, LC Cesa, CH Doss, SP Rowe, V Vasquez, G Tamayo-Castillo, T Cierpicki, CL Brooks III, DH Sherman and AK Mapp. Sekikaic Acid and Lobaric Acid Target a Dynamic Interface of the Coactivator CBP/p300. Angew Chem Int Ed Engl, 2012, 51:11258-62.  PubMed
  1. RV Mannige, CL Brooks III and EI Shakhnovich. A universal trend among proteomes indicates an oily last common ancestor. PLoS Comput Biol, 2012, 8:e1002839. PMCID: 3531291.  PubMed
  1. ER May and CL Brooks III. On the morphology of viral capsids: elastic properties and buckling transitions. J Phys Chem B, 2012, 116:8604-9. PMCID: 3395760.  PubMed
  1. ER May, J Feng and CL Brooks III. Exploring the symmetry and mechanism of virus capsid maturation via an ensemble of pathways. Biophys J, 2012, 102:606-12. PMCID: 3274788.  PubMed
  1. WH Roos, I Gertsman, ER May, CL Brooks III, JE Johnson and GJ Wuite. Mechanics of bacteriophage maturation. Proc Natl Acad Sci U S A, 2012, 109:2342-7. PMCID: 3289345.  PubMed
  1. H Vashisth and CL Brooks III. Conformational Sampling of Maltose-transporter Components in Cartesian Collective Variables is Governed by the Low-frequency Normal Modes. J Phys Chem Lett, 2012, 3:3379-3384. PMCID: 3505029.  PubMed
  1. H Vashisth, G Skiniotis and CL Brooks III. Using enhanced sampling and structural restraints to refine atomic structures into low-resolution electron microscopy maps. Structure, 2012, 20:1453-62. PMCID: 3438525.  PubMed
  1. JD Yesselman, DJ Price, JL Knight and CL Brooks III. MATCH: an atom-typing toolset for molecular mechanics force fields. J Comput Chem, 2012, 33:189-202. PMCID: 3228871.  PubMed

Book Chapter

  1. ER May, K Arora, R Mannige, HD Nguyen and CL Brooks III. Multiscale Modeling of Virus Structure, Assembly and Dynamics. In Computational Modeling of Biological Systems: From Molecules to Pathways. Edited by N Dokholyan. Published by Springer. Volume: VI, In Computational Modeling of Biological Systems: From Molecules to Pathways

2011

Journal Article

  1. EJ Arthur, JD Yesselman and CL Brooks III. Predicting extreme pK(a) shifts in staphylococcal nuclease mutants with constant pH molecular dynamics. Proteins, 2011, 79:3276-86. PMCID: 3213318.  PubMed
  1. MH Bailor, AM Mustoe, CL Brooks III and HM Al-Hashimi. Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation. Curr Opin Struct Biol, 2011, 21:296-305.  PubMed
  1. MH Bailor, AM Mustoe, CL Brooks III and HM Al-Hashimi. 3D maps of RNA interhelical junctions. Nat Protoc, 2011, 6:1536-45.  PubMed
  1. CD Eichhorn, J Feng, KC Suddala, NG Walter, CL Brooks III and HM Al-Hashimi. Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch. Nucleic Acids Res, 2011, 40:1345-55. PMCID: 3273816.  PubMed
  1. J Feng, NG Walter and CL Brooks III. Cooperative and directional folding of the preQ1 riboswitch aptamer domain. J Am Chem Soc, 2011, 133:4196-9. PMCID: 3109358.  PubMed
  1. GB Goh, EB Garcia-Moreno and CL Brooks III. The high dielectric constant of staphylococcal nuclease is encoded in its structural architecture. J Am Chem Soc, 2011, 133:20072-5. PMCID: 3241862.  PubMed
  1. JL Knight and CL Brooks III. Surveying implicit solvent models for estimating small molecule absolute hydration free energies. J Comput Chem, 2011, 32:2909-23. PMCID: 3142295.  PubMed
  1. JL Knight and CL Brooks III. Applying efficient implicit nongeometric constraints in alchemical free energy simulations. J Comput Chem, 2011, 32:3423-32. PMCID: 3196384.  PubMed
  1. JL Knight and CL Brooks III. Multi-Site lambda-dynamics for simulated Structure-Activity Relationship studies. J Chem Theor Comput, 2011, 7:2728-2739. PMCID: 3223982.  PubMed
  1. V Lopez-Mejias, JL Knight, CL Brooks III and AJ Matzger. On the mechanism of crystalline polymorph selection by polymer heteronuclei. Langmuir, 2011, 27:7575-9. PMCID: 3124555.  PubMed
  1. ER May, A Aggarwal, WS Klug and CL Brooks III. Viral capsid equilibrium dynamics reveals nonuniform elastic properties. Biophys J, 2011, 100:L59-61. PMCID: 3117158.  PubMed
  1. ER May and CL Brooks III. Determination of viral capsid elastic properties from equilibrium thermal fluctuations. Phys Rev Lett, 2011, 106:188101.  PubMed
  1. AM Mustoe, MH Bailor, RM Teixeira, CL Brooks III and HM Al-Hashimi. New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation. Nucleic Acids Res, 2011, 40:892-904. PMCID: 3258142.  PubMed
  1. O Rahaman, TP Estrada, DJ Doren, M Taufer, CL Brooks III and RS Armen. Evaluation of several two-step scoring functions based on linear interaction energy, effective ligand size, and empirical pair potentials for prediction of protein-ligand binding geometry and free energy. J Chem Inf Model, 2011, 51:2047-65. PMCID: 3183351.  PubMed
  1. BS Strunk, CR Loucks, M Su, H Vashisth, S Cheng, J Schilling, CL Brooks III, K Karbstein and G Skiniotis. Ribosome assembly factors prevent premature translation initiation by 40S assembly intermediates. Science, 2011, 333:1449-53. PMCID: 3402165.  PubMed
  1. T Wymore, B Chen, HB Nichiolas Jr, AJ Ropelewski and CL Brooks III. The evolvability of plant sesquiterpene synthases. Molecular Informatics, 2011, 30:896-906.
  1. BW Zhang, L Brunetti and CL Brooks III. Probing pH-dependent dissociation of HdeA dimers. J Am Chem Soc, 2011, 133:19393-8. PMCID: 3227773.  PubMed

Book Chapter

  1. K Arora and CL Brooks III. Exploring the functional landscape of biomolecular machines via elastic network normal mode analysis. In Molecular Machines in Biology. Edited by J Frank. Published by Cambridge University Press (New York). Volume: 1, In Molecular Machines in Biology

2010

Journal Article

  1. RS Armen, SM Schiller and CL Brooks III. Steric and thermodynamic limits of design for the incorporation of large unnatural amino acids in aminoacyl-tRNA synthetase enzymes. Proteins, 2010, 78:1926-38.  PubMed
  1. DL Bostick and CL Brooks III. Selective complexation of K+ and Na+ in simple polarizable ion-ligating systems. J Am Chem Soc, 2010, 132:13185-7. PMCID: 3051181.  PubMed
  1. RD Hills Jr, SV Kathuria, LA Wallace, IJ Day, CL Brooks III and CR Matthews. Topological frustration in beta alpha-repeat proteins: sequence diversity modulates the conserved folding mechanisms of alpha/beta/alpha sandwich proteins. J Mol Biol, 2010, 398:332-50. PMCID: 2862464.  PubMed
  1. JS Hirschi, K Arora, CL Brooks III and VL Schramm. Conformational dynamics in human purine nucleoside phosphorylase with reactants and transition-state analogues. J Phys Chem B, 2010, 114:16263-72. PMCID: 3005859.  PubMed
  1. RV Mannige and CL Brooks III. Periodic table of virus capsids: implications for natural selection and design. PLoS One, 2010, 5:e9423. PMCID: 2831995.  PubMed
  1. ER May, RS Armen, AM Mannan and CL Brooks III. The flexible C-terminal arm of the Lassa arenavirus Z-protein mediates interactions with multiple binding partners. Proteins, 2010, 78:2251-64.  PubMed
  1. M Michino, J Chen, RC Stevens and CL Brooks III. FoldGPCR: structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A. Proteins, 2010, 78:2189-201.  PubMed
  1. K Yoshimoto, K Arora and CL Brooks III. Hexameric helicase deconstructed: interplay of conformational changes and substrate coupling. Biophys J, 2010, 98:1449-57. PMCID: 2856183.  PubMed
  1. J Zimmermann, FE Romesberg, CL Brooks III and IF Thorpe. Molecular description of flexibility in an antibody combining site. J Phys Chem B, 2010, 114:7359-70. PMCID: 2892760.  PubMed

Book Chapter

  1. J Chen, W Im and CL Brooks III. Implicit solvent force field optimization. In Modeling Solvent Environments. Edited by M Feig. Published by Wiley-VCH (Germany). In Modeling Solvent Environments

2009

Journal Article

  1. RS Armen, J Chen and CL Brooks III. An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics. J Chem Theor Comput, 2009, 5:2909-2923. PMCID: 2772076.  PubMed
  1. K Arora and CL Brooks III. Functionally important conformations of the Met20 loop in dihydrofolate reductase are populated by rapid thermal fluctuations. J Am Chem Soc, 2009, 131:5642-7. PMCID: 2889193.  PubMed
  1. DL Bostick, K Arora and CL Brooks III. K+/Na+ selectivity in toy cation binding site models is determined by the 'host'. Biophys J, 2009, 96:3887-96. PMCID: 2712193.  PubMed
  1. DL Bostick and CL Brooks III. Statistical determinants of selective ionic complexation: ions in solvent, transport proteins, and other "hosts". Biophys J, 2009, 96:4470-92. PMCID: 2894556.  PubMed
  1. BR Brooks, CL Brooks III, AD Mackerell Jr, L Nilsson, RJ Petrella, B Roux, Y Won, G Archontis, C Bartels, S Boresch, A Caflisch, L Caves, Q Cui, AR Dinner, M Feig, S Fischer, J Gao, M Hodoscek, W Im, K Kuczera, T Lazaridis, J Ma, V Ovchinnikov, E Paci, RW Pastor, CB Post, JZ Pu, M Schaefer, B Tidor, RM Venable, HL Woodcock, X Wu, W Yang, DM York and M Karplus. CHARMM: the biomolecular simulation program. J Comput Chem, 2009, 30:1545-614. PMCID: 2810661.  PubMed
  1. M Carrillo-Tripp, CM Shepherd, IA Borelli, S Venkataraman, G Lander, P Natarajan, JE Johnson, CL Brooks III and VS Reddy. VIPERdb2: an enhanced and web API enabled relational database for structural virology. Nucleic Acids Res, 2009, 37:D436-42. PMCID: 2686430.  PubMed
  1. RD Hills and CL Brooks III. Insights from coarse-grained Go models for protein folding and dynamics. Int J Mol Sci, 2009, 10:889-905. PMCID: 2672008.  PubMed
  1. JL Knight and CL Brooks III. Lambda-dynamics free energy simulation methods. J Comput Chem, 2009, 30:1692-700. PMCID: 2730455.  PubMed
  1. JL Knight and CL Brooks III. Validating CHARMM parameters and exploring charge distribution rules in structure-based drug design. J Chem Theor Comput, 2009, 5:1680-1691. PMCID: 2719862.  PubMed
  1. RV Mannige and CL Brooks III. Geometric considerations in virus capsid size specificity, auxiliary requirements, and buckling. Proc Natl Acad Sci U S A, 2009, 106:8531-6. PMCID: 2688982.  PubMed
  1. M Michino, E Abola, CL Brooks III, JS Dixon, J Moult and RC Stevens. Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nature Reviews Drug Discovery, 2009, 8:455-63. PMCID: 2728591.  PubMed
  1. M Michino and CL Brooks III. Predicting structurally conserved contacts for homologous proteins using sequence conservation filters. Proteins, 2009, 77:448-53. PMCID: 2740814.  PubMed
  1. HD Nguyen, VS Reddy and CL Brooks III. Invariant polymorphism in virus capsid assembly. J Am Chem Soc, 2009, 131:2606-14. PMCID: 2768263.  PubMed
  1. M Taufer, R Armen, J Chen, P Teller and CL Brooks III. Computational multiscale modeling in protein--ligand docking. IEEE Eng Med Biol Mag, 2009, 28:58-69.  PubMed
  1. L Zhong, JF Matthews, PI Hansen, MF Crowley, JM Cleary, RC Walker, MR Nimlos, CL Brooks III, WS Adney, ME Himmel and JW Brady. Computational simulations of the Trichoderma reesei cellobiohydrolase I acting on microcrystalline cellulose Ibeta: the enzyme-substrate complex. Carbohydrate Research, 2009, 344:1984-92.  PubMed

2008

Journal Article

  1. L Bu and CL Brooks III. De novo prediction of the structures of M. tuberculosis membrane proteins. J Am Chem Soc, 2008, 130:5384-5.  PubMed
  1. L Bu, M Michino, RM Wolf and CL Brooks III. Improved model building and assessment of the Calcium-sensing receptor transmembrane domain. Proteins, 2008, 71:215-26.  PubMed
  1. M Carrillo-Tripp, CL Brooks III and VS Reddy. A novel method to map and compare protein-protein interactions in spherical viral capsids. Proteins, 2008, 73:644-655.  PubMed
  1. J Chen and CL Brooks III. Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions. Phys Chem Chem Phys, 2008, 10:471-81.  PubMed
  1. J Chen, CL Brooks III and J Khandogin. Recent advances in implicit solvent-based methods for biomolecular simulations. Curr Opin Struct Biol, 2008, 18:140-8. PMCID: 2386893.  PubMed
  1. 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, 112:242-9. PMCID: 2561919.  PubMed
  1. RD Hills Jr and CL Brooks III. Coevolution of function and the folding landscape: correlation with density of native contacts. Biophys J, 2008, 95:L57-9. PMCID: 2567933.  PubMed
  1. RD Hills Jr and CL Brooks III. Subdomain competition, cooperativity, and topological frustration in the folding of CheY. J Mol Biol, 2008, 382:485-95. PMCID: 2564871.  PubMed
  1. 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, 193:68-76. PMCID: 2546517.  PubMed
  1. RV Mannige and CL Brooks III. Tilable nature of virus capsids and the role of topological constraints in natural capsid design. Phys Rev E Stat Nonlin Soft Matter Phys, 2008, 77:051902. PMCID: 2756041.  PubMed
  1. HD Nguyen and CL Brooks III. Generalized structural polymorphism in self-assembled viral particles. Nano Lett, 2008, 8:4574-81. PMCID: 2772182.  PubMed
  1. 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, 29:820-31.  PubMed
  1. 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 U S A, 2008, 105:5891-6. PMCID: 2311355.  PubMed
  1. 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.

2007

Journal Article

  1. 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 U S A, 2007, 104:18496-501. PMCID: 2141805.  PubMed
  1. 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 U S A, 2007, 104:9260-5. PMCID: 1890482.  PubMed
  1. 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:L103-5. PMCID: 1877791.  PubMed
  1. DL Bostick and CL Brooks III. Deprotonation by dehydration: the origin of ammonium sensing in the AmtB channel. PLoS Comput Biol, 2007, 3:e22. PMCID: 1796661.  PubMed
  1. L Bu, W Im and CL Brooks III. Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations. Biophys J, 2007, 92:854-63. PMCID: 1779983.  PubMed
  1. J Chen and CL Brooks III. Can molecular dynamics simulations provide high-resolution refinement of protein structure. Proteins, 2007, 67:922-30.  PubMed
  1. J Chen and CL Brooks III. Critical importance of length-scale dependence in implicit modeling of hydrophobic interactions. J Am Chem Soc, 2007, 129:2444-5. PMCID: 2551325.  PubMed
  1. RD Hills Jr and CL Brooks III. Hydrophobic cooperativity as a mechanism for amyloid nucleation. J Mol Biol, 2007, 368:894-901. PMCID: 1997311.  PubMed
  1. J Khandogin and CL Brooks III. Linking folding with aggregation in Alzheimer's beta-amyloid peptides. Proc Natl Acad Sci U S A, 2007, 104:16880-5. PMCID: 2040412.  PubMed
  1. 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, 129:3056-7. PMCID: 2546516.  PubMed
  1. 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, 16:1087-100. PMCID: 2206655.  PubMed
  1. HD Nguyen, VS Reddy and CL Brooks III. Deciphering the kinetic mechanism of spontaneous self-assembly of icosahedral capsids. Nano Lett, 2007, 7:338-44.  PubMed
  1. M Taufer, A Kerstens, T Estrada, D Flores, R Zamudio, P Teller, R Armen and CL Brooks III. Moving Volunteer Computing towards Knowledge-Constructed, Dynamically-Adaptive Modeling and Scheduling. IDPDS, 2007, :1-8.
  1. IF Thorpe and CL Brooks III. Molecular evolution of affinity and flexibility in the immune system. Proc Natl Acad Sci U S A, 2007, 104:8821-6. PMCID: 1885586.  PubMed

Book Chapter

  1. J Khandogin and CL Brooks III. Molecular Simulations of pH-Mediated Biological Processes. In Annual Reports in Computational Chemistry. Edited by D Spellmeyer, R Wheeler. Published by Elsevier (New York, NY). Volume: 3, In Annual Reports in Computational Chemistry

2006

Journal Article

  1. 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, 128:3728-36.  PubMed
  1. J Khandogin and CL Brooks III. Toward the accurate first-principles prediction of ionization equilibria in proteins. Biochemistry, 2006, 45:9363-73.  PubMed
  1. J Khandogin, J Chen and CL Brooks III. Exploring atomistic details of pH-dependent peptide folding. Proc Natl Acad Sci U S A, 2006, 103:18546-50.  PubMed
  1. IV Khavrutskii, K Arora and CL Brooks III. Harmonic Fourier beads method for studying rare events on rugged energy surfaces. J Chem Phys, 2006, 125:174108.  PubMed
  1. 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, 124:194903.  PubMed
  1. 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, 82:106-20.  PubMed
  1. S Patel and CL Brooks III. Fluctuating charge force fields: Recent developments and applications from small molecules to macromolecular biological systems. Molecular Simulation, 2006, 32:231-249.  PubMed
  1. SA Patel and CL Brooks III. Revisiting the hexane-water interface via molecular dynamics simulations using nonadditive alkane-water potentials. J Chem Phys, 2006, 124:204706.  PubMed
  1. 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:D386-9.  PubMed
  1. 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, 80:10395-406.  PubMed
  1. 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
  1. 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, 15:2190-200.  PubMed
  1. M Taufer, C An, A Kerstens and CL Brooks III. Predictor@Home: A "protein structure prediction supercomputer" based on global computing. Ieee Transactions on Parallel and Distributed Systems, 2006, 17:786-796.
  1. 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, 45:4463-73.  PubMed
  1. 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 U S A, 2006, 103:13722-7.  PubMed

Book Chapter

  1. F Tama and CL Brooks III. Unveiling molecular mechanisms of biological functions in large macromolecular assemblies using elastic network normal mode analysis. In Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems. Edited by Q Cui, I Bahar. Series title: Mathematical and Computational Biology Series. Published by Chapman & Hall/CRC (Boca Raton, FL). In Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems

2005

Journal Article

  1. CL Brooks III. Editorial. J Comput Chem, 2005, 26:1667.  PubMed
  1. J Chen, W Im and CL Brooks III. Application of torsion angle molecular dynamics for efficient sampling of protein conformations. J Comput Chem, 2005, 26:1565-78.  PubMed
  1. 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, 31:59-64.  PubMed
  1. 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, 348:219-30.  PubMed
  1. 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, 127:4668-74.  PubMed
  1. O Guvench, DJ Price and CL Brooks III. Receptor rigidity and ligand mobility in trypsin-ligand complexes. Proteins, 2005, 58:407-17.  PubMed
  1. 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 U S A, 2005, 102:6771-6.  PubMed
  1. 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
  1. J Khandogin and CL Brooks III. Constant pH Molecular Dynamics with Proton Tautomerism. Biophys J, 2005, 89:141-57.  PubMed
  1. 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, 438:318-24.  PubMed
  1. P Natarajan, GC Lander, CM Shepherd, VS Reddy, CL Brooks III and JE Johnson. Exploring icosahedral virus structures with VIPER. Nat Rev Microbiol, 2005, 3:809-17.  PubMed
  1. 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, 122:24508.  PubMed
  1. 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, 123:164502.  PubMed
  1. 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, 26:1529-41.  PubMed
  1. 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, 345:299-314.  PubMed
  1. 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, 345:837-54.  PubMed
  1. M Taufer, M Crowley, DJ Price, AA Chien and CL Brooks III. Study of a highly accurate and fast protein-ligand docking method based on molecular dynamics. Concurrency and Computation-Practice & Experience, 2005, 17:1627-1641.
  1. M Taufer, PJ Teller, DP Anderson and CL Brooks III. Metrics for effective resource management in global computing environments. First International Conference on e-Science and Grid Computing, Proceedings, 2005, :204-211.
  1. IF Thorpe and CL Brooks III. Conformational substates modulate hydride transfer in dihydrofolate reductase. J Am Chem Soc, 2005, 127:12997-3006.  PubMed
  1. J Trylska, JA McCammon and C Brooks III. Exploring assembly energetics of the 30S ribosomal subunit using an implicit solvent approach. J Am Chem Soc, 2005, 127:11125-33.  PubMed

Conference Proceedings

  1. M Taufer, C An, A Kerstens and C Brooks III. Predictor@Home: A "Protein Structure Prediction Supercomputer" Based on Public-Resource Computing. In Proceedings of the 4th IEEE International Workshop on High Performance Computational Biology (HiCOMB 2005) (Denver, Colorado).
  1. M Taufer, D Anderson, P Cicotti and C Brooks III. Homogeneous Redundancy: a Technique to Ensure Integrity of Molecular Simulation Results Using Public Computing. In Proceedings of 14th Heterogeneous Computing Workshop (HCW 2005) (Denver, Colorado).

2004

Journal Article

  1. 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, 29:243-57.  PubMed
  1. J Chen, W Im and CL Brooks III. Refinement of NMR structures using implicit solvent and advanced sampling techniques. J Am Chem Soc, 2004, 126:16038-47.  PubMed
  1. BN Dominy, H Minoux and CL Brooks III. An electrostatic basis for the stability of thermophilic proteins. Proteins, 2004, 57:128-41.  PubMed
  1. 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, 14:217-24.  PubMed
  1. M Feig, W Im and CL Brooks III. Implicit solvation based on generalized Born theory in different dielectric environments. J Chem Phys, 2004, 120:903-11.  PubMed
  1. 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, 22:377-95.  PubMed
  1. 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, 25:265-84.  PubMed
  1. P Ferrara, H Gohlke, DJ Price, G Klebe and CL Brooks III. Assessing scoring functions for protein-ligand interactions. J Med Chem, 2004, 47:3032-47.  PubMed
  1. 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, 25:1005-14.  PubMed
  1. 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, 337:513-9.  PubMed
  1. J Karanicolas and C Brooks III. An evolution of minimalist models for protein folding: from the behavior of protein-like polymers to protein function. Biosilico, 2004, 2:127-133.
  1. 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 U S A, 2004, 101:3432-7.  PubMed
  1. MS Lee, FR Salsbury Jr and CL Brooks III. Constant-pH molecular dynamics using continuous titration coordinates. Proteins, 2004, 56:738-52.  PubMed
  1. AD MacKerell Jr, M Feig and CL Brooks III. Improved treatment of the protein backbone in empirical force fields. J Am Chem Soc, 2004, 126:698-9.  PubMed
  1. 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, 25:1400-15.  PubMed
  1. 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.
  1. 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, 25:1-15.  PubMed
  1. 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, 25:1504-14.  PubMed
  1. DJ Price and CL Brooks III. A modified TIP3P water potential for simulation with Ewald summation. J Chem Phys, 2004, 121:10096-103.  PubMed
  1. 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, 340:571-85.  PubMed
  1. 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, 337:985-99.  PubMed
  1. 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, 147:315-26.  PubMed
  1. IF Thorpe and CL Brooks III. The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase. Proteins, 2004, 57:444-57.  PubMed
  1. J Trylska, R Konecny, F Tama, CL Brooks III and JA McCammon. Ribosome motions modulate electrostatic properties. Biopolymers, 2004, 74:423-31.  PubMed

Book Chapter

  1. V Reddy, P Natarajan, G Lander, C Qu, C Brooks III and J Johnson. Virus Particle Explorer (VIPER): A repository of virus capsid structures. In Conformational proteomics of macromolecular Architecture. Edited by RH Cheng, L Hammer. Published by World Scientific Pub Co. (Singapore). Volume: Chpt. 20, In Conformational proteomics of macromolecular Architecture

Conference Proceedings

  1. D Kondo, M Taufer, C Brooks III, H Casanova and A Chien. Characterizing and Evaluating Desktop Grids: An Empirical Study. In IEEE/ACM International Parallel and Distributed Processing Symposium (Santa Fe, New Mexico).
  1. M Taufer, M Crowley, D Price, A Chien and C Brooks III. Study of an Accurate and Fast Protein-Ligand Docking Algorithm based on Molecular Dynamics. In Proceedings of the 3rd IEEE International Workshop on High Performance Computational Biology (HiCOMB 2004) (Santa Fe, New Mexico.).

2003

Journal Article

  1. 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, 13:143-145.
  1. 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, 17:755-63.  PubMed
  1. 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, 107:2831-2836.
  1. 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, 85:2900-18.  PubMed
  1. W Im, MS Lee and CL Brooks III. Generalized born model with a simple smoothing function. J Comput Chem, 2003, 24:1691-702.  PubMed
  1. 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 U S A, 2003, 100:3954-9.  PubMed
  1. 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, 334:309-25.  PubMed
  1. J Karanicolas and CL Brooks III. The importance of explicit chain representation in protein folding models: an examination of Ising-like models. Proteins, 2003, 53:740-7.  PubMed
  1. 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, 24:1348-56.  PubMed
  1. 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 U S A, 2003, 100:13916-21.  PubMed
  1. TH Rod and CL Brooks III. How dihydrofolate reductase facilitates protonation of dihydrofolate. J Am Chem Soc, 2003, 125:8718-9.  PubMed
  1. TH Rod, JL Radkiewicz and CL Brooks III. Correlated motion and the effect of distal mutations in dihydrofolate reductase. Proc Natl Acad Sci U S A, 2003, 100:6980-5.  PubMed
  1. 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, 4:848-55.  PubMed
  1. 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, 119:5722-5729.
  1. 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 U S A, 2003, 100:9319-23.  PubMed
  1. 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, 107:14042-14051.
  1. 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, 24:1549-62.  PubMed

2002

Journal Article

  1. CL Brooks III. Viewing protein folding from many perspectives. Proc Natl Acad Sci U S A, 2002, 99:1099-100.  PubMed
  1. CL Brooks III. Protein and peptide folding explored with molecular simulations. Acc Chem Res, 2002, 35:447-54.  PubMed
  1. CL Brooks III. Protein folding: with a little help. Nature, 2002, 420:33-4.  PubMed
  1. KV Damodaran, VS Reddy, JE Johnson and CL Brooks III. A general method to quantify quasi-equivalence in icosahedral viruses. J Mol Biol, 2002, 324:723-37.  PubMed
  1. BN Dominy and CL Brooks III. Identifying native-like protein structures using physics-based potentials. J Comput Chem, 2002, 23:147-60.  PubMed
  1. 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, 319:541-54.  PubMed
  1. M Feig and CL Brooks III. Evaluating CASP4 predictions with physical energy functions. Proteins, 2002, 49:232-45.  PubMed
  1. A Fiser, M Feig, CL Brooks III and A Sali. Evolution and physics in comparative protein structure modeling. Acc Chem Res, 2002, 35:413-21.  PubMed
  1. J Karanicolas and CL Brooks III. The origins of asymmetry in the folding transition states of protein L and protein G. Protein Sci, 2002, 11:2351-61.  PubMed
  1. MS Lee, FR Salsbury Jr and CL Brooks III. Novel generalized Born methods. J Chem Phys, 2002, 116:10606-10614.
  1. DJ Price and CL Brooks III. Modern protein force fields behave comparably in molecular dynamics simulations. J Comput Chem, 2002, 23:1045-57.  PubMed
  1. JE Shea, JN Onuchic and CL Brooks III. Probing the folding free energy landscape of the Src-SH3 protein domain. Proc Natl Acad Sci U S A, 2002, 99:16064-8.  PubMed
  1. F Tama and CL Brooks III. The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus. J Mol Biol, 2002, 318:733-47.  PubMed
  1. 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, 321:297-305.  PubMed

2001

Journal Article

  1. CL Brooks III, JN Onuchic and DJ Wales. Perspectives: statistical thermodynamics. Taking a walk on a landscape. Science (Washington, DC, United States), 2001, 293:612-613.
  1. 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, 105:9316-9322.
  1. 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, 75:11943-7.  PubMed
  1. O Roche, R Kiyama and CL Brooks III. Ligand-protein database: linking protein-ligand complex structures to binding data. J Med Chem, 2001, 44:3592-8.  PubMed
  1. 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, 44:448-59.  PubMed
  1. KA Sharp and CL Brooks III. Theory and simulation: Old wine in new bottles. Curr Opin Struct Biol, 2001, 11:209-211.

Book Chapter

  1. S Banba, Z Guo and CL Brooks III. New free energy based methods for ligand binding from detailed structure-function to multiple-ligand screening. In Free Energy Calculations in Rational Drug Design. Edited by M Reddy, M Erion. Published by Kluwar Academic/Plenum Publishers (New York). Volume: 1, In Free Energy Calculations in Rational Drug Design
  1. JE Shea and CL Brooks III. From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding. In Annu Rev Phys Chem. Edited by HL Strauss. Published by Annual Reviews (Palo Alto). Volume: 52, In Annu Rev Phys Chem

2000

Journal Article

  1. S Banba and CL Brooks III. Free energy screening of small ligands binding to an artificial protein cavity. J Chem Phys, 2000, 113:3423-3433.
  1. 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, 104:6903-6910.
  1. 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, 104:12378-12383.
  1. 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, 41:86-97.  PubMed
  1. JL Radkiewicz and CL Brooks III. Protein Dynamics in Enzymatic Catalysis: Exploration of Dihydrofolate Reductase. J Am Chem Soc, 2000, 122:225-231.
  1. J Shea, JN Onuchic and CL Brooks III. Energetic frustration and the nature of the transition state in protein folding. J Chem Phys, 2000, 113:7663-7671.
  1. 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, 104:9554-9563.

1999

Journal Article

  1. BD Bursulaya and CL Brooks III. Folding free energy surface of a three-stranded b-sheet protein. J Am Chem Soc, 1999, 121:9947-9951.
  1. BN Dominy and CL Brooks III. Development of a Generalized Born Model Parametrization for Proteins and Nucleic Acids. J Phys Chem B, 1999, 103:3765-3773.
  1. 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, 36:318-31.  PubMed
  1. 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, 35:447-52.  PubMed
  1. 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 U S A, 1999, 96:12512-7.  PubMed

Book Chapter

  1. JD Hirst, B Dominy, Z Guo, M Vieth and CL Brooks III. Conformational and energetic aspects of receptor-ligand recognition. In Rational Drug Design. Series title: ACS Symposium Series. Volume: 719, In Rational Drug Design

1998

Journal Article

  1. CL Brooks III. Simulations of protein folding and unfolding. Curr Opin Struct Biol, 1998, 8:222-6.  PubMed
  1. CL Brooks III, M Gruebele, JN Onuchic and PG Wolynes. Chemical physics of protein folding. Proc Natl Acad Sci U S A, 1998, 95:11037-8.  PubMed
  1. 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, 120:1920-1921.
  1. 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, 102:2032-2036.
  1. 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, 74:546-58.  PubMed
  1. J 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, 109:2895-2903.
  1. FB Sheinerman and CL Brooks III. Molecular picture of folding of a small alpha/beta protein. Proc Natl Acad Sci U S A, 1998, 95:1562-7.  PubMed
  1. FB Sheinerman and CL Brooks III. Calculations on folding of segment B1 of streptococcal protein G. J Mol Biol, 1998, 278:439-56.  PubMed
  1. 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, 12:563-72.  PubMed
  1. M Vieth, JD Hirst, BN Dominy, H Daigler and CL Brooks III. Assessing search strategies for flexible docking. J Comput Chem, 1998, 19:1623-1631.
  1. M Vieth, JD Hirst, A Kolinski and CL Brooks III. Assessing energy functions for flexible docking. J Comput Chem, 1998, 19:1612-1622.

Book Chapter

  1. A MacKerell Jr, B Brooks, CL Brooks III, L Nilsson, B Roux, Y Won and M Karplus. CHARMM: The energy function and its parameterization. In Encyclopedia of Computational Chemistry. Edited by P Schleyer, N Allinger, T Clark, J Gasteiger, P Kollman, H Schaefer III, P Schreiner. Published by John Wiley & Sons, Ltd. (Chichester, UK). Volume: 1, In Encyclopedia of Computational Chemistry

1997

Journal Article

  1. Z Guo and CL Brooks III. Thermodynamics of protein folding: a statistical mechanical study of a small all-beta protein. Biopolymers, 1997, 42:745-57.  PubMed
  1. Z Guo, CL Brooks III and EM Boczko. Exploring the folding free energy surface of a three-helix bundle protein. Proc Natl Acad Sci U S A, 1997, 94:10161-6.  PubMed
  1. 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, 101:4821-4827.
  1. FB Sheinerman and CL Brooks III. A molecular dynamics simulation study of segment B1 of protein G. Proteins, 1997, 29:193-202.  PubMed
  1. WA Shirley and CL Brooks III. Curious structure in "canonical" alanine-based peptides. Proteins, 1997, 28:59-71.  PubMed
  1. 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, 106:9265-9269.

1996

Journal Article

  1. CL Brooks III. Helix-Coil Kinetics: Folding Time Scales for Helical Peptides from a Sequential Kinetic Model. J Phys Chem, 1996, 100:2546-9.
  1. CL Brooks III, CB Post and P Rossky. Biography of Martin Karplus. J Phys Chem, 1996, 100:2458.
  1. JD Hirst, DM Hirst and CL Brooks III. Ab Initio Calculations of the Excited States of Formamide. J Phys Chem, 1996, 100:13487-13491.
  1. JD Hirst, M Vieth, J Skolnick and CL Brooks III. Predicting leucine zipper structures from sequence. Protein Eng, 1996, 9:657-62.  PubMed
  1. ME Karpen and CL Brooks III. Modeling protein conformation by molecular mechanics and dynamics. Protein Structure Prediction, 1996, :229-261.
  1. X Kong and CL Brooks III. l-Dynamics: a new approach to free energy calculations. J Chem Phys, 1996, 105:2314-2423.
  1. 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, 100:2698-705.
  1. T Simonson and CL Brooks III. Charge Screening and the Dielectric Constant of Proteins: Insights from Molecular Dynamics. J Am Chem Soc, 1996, 118:8452-8458.
  1. 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 Series in Discrete Mathematics and Theoretical Computer Science, 1996, 23:233-236.
  1. 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, 0:653-62.  PubMed
  1. 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, 259:560-72.  PubMed

1995

Journal Article

  1. EM Boczko and CL Brooks III. First-principles calculation of the folding free energy of a three-helix bundle protein. Science, 1995, 269:393-6.  PubMed
  1. CL Brooks III. Methodological advances in molecular dynamics simulations of biological systems. Curr Opin Struct Biol, 1995, 5:211-5.  PubMed
  1. JD Hirst and CL Brooks III. Molecular dynamics simulations of isolated helices of myoglobin. Biochemistry, 1995, 34:7614-21.  PubMed
  1. FB Sheinerman and CL Brooks III. 310 Helices in Peptides and Proteins As Studied by Modified Zimm-Bragg Theory. J Am Chem Soc, 1995, 117:10098-103.
  1. 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, 251:448-67.  PubMed
  1. WS Young and CL Brooks III. Dynamic load balancing algorithms for replicated data molecular dynamics. J Comput Chem, 1995, 16:715-22.

Book Chapter

  1. J Skolnick, M Vieth, A Kolinski and CL Brooks III. De novo simulations of the folding of GCN4 and its mutants. In Jerusalem Symposia on Quantum Chemistry and Biochemistry. Edited by A Pullman etal. Published by Kluwar Academic Publishers (Netherlands). Volume: 27, In Jerusalem Symposia on Quantum Chemistry and Biochemistry

1994

Journal Article

  1. JD Hirst and CL Brooks III. Helicity, circular dichroism and molecular dynamics of proteins. J Mol Biol, 1994, 243:173-8.  PubMed
  1. C Tsoo and C Brooks III. Cluster Structure Determination Using Gaussian Density Annealing. J Chem Phys, 1994, 101:6405-6411.
  1. 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, 237:361-7.  PubMed
  1. 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 Comput Chem, 1994, 15:44-53.

1993

Journal Article

  1. EM Boczko and CL Brooks III. Constant-temperature free energy surfaces for physical and chemical processes. J Phys Chem, 1993, 97:4509-13.
  1. C Brooks III and DA Case. Simulations of peptide conformational dynamics and thermodynamics. Chem Rev, 1993, 93:2487-502.
  1. CL Brooks III. Molecular simulations of peptide and protein unfolding: In quest of a molten globule. Curr Opin Struct Biol, 1993, 3:92-8.
  1. CL Brooks III and L Nilsson. Promotion of helix formation in peptides dissolved in alcohol and water-alcohol mixtures. J Am Chem Soc, 1993, 115:11034-5.
  1. 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, 32:412-20.  PubMed
  1. J Skolnick, A Kolinski, CL Brooks III, A Godzik and A Rey. A method for predicting protein structure from sequence. Curr Biol, 1993, 3:414-23.  PubMed
  1. SF Sneddon and CL Brooks III. Protein motions: structural and functional aspects. Mol Struct Biol, 1993, :114-63.

1992

Journal Article

  1. CL Brooks III. Characterization of "native" apomyoglobin by molecular dynamics simulation. J Mol Biol, 1992, 227:375-80.  PubMed
  1. 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, 114:2062-72.
  1. SF Sneddon and CL Brooks III. The conformations of proline-linked donor-acceptor systems. J Am Chem Soc, 1992, 114:8220-5.
  1. 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, 96:3864-70.
  1. DJ Tobias, SF Sneddon and CL Brooks III. Stability of a model beta-sheet in water. J Mol Biol, 1992, 227:1244-52.  PubMed

1991

Journal Article

  1. CL Brooks III, WS Young and DJ Tobias. Molecular Simulations on Supercomputers. Intl J Supercomput Appl, 1991, 5:98-112.
  1. T Head-Gordon and CL Brooks III. Virtual rigid body dynamics. Biopolymers, 1991, 31:77-100.  PubMed
  1. 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, 113:5989-97.
  1. 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.
  1. 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, 113:2295-301.
  1. DR McKelvey, CL Brooks and M Mokotoff. A CHARMM analysis of the conformations of the metastasis-inhibiting laminin pentapeptide. J Protein Chem, 1991, 10:265-71.  PubMed
  1. 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 Comput Chem, 1991, 12:1270-7.
  1. DJ Tobias and CL Brooks III. Thermodynamics and mechanism of alpha helix initiation in alanine and valine peptides. Biochemistry, 1991, 30:6059-70.  PubMed
  1. DJ Tobias, JE Mertz and CL Brooks III. Nanosecond time scale folding dynamics of a pentapeptide in water. Biochemistry, 1991, 30:6054-8.  PubMed

Book Chapter

  1. CL Brooks III. Semiclassical methods for large molecules of biological importance. In Theor. Models Chem. Bonding. Published by Springer-Verlag. Volume: 4, In Theor. Models Chem. Bonding
  1. S Sneddon and CL Brooks III. Protein Motions: Structural and Functional Aspects. In Molecular Structures in Biology. Edited by R Diamond. Published by Oxford University Press (Oxford, England). In Molecular Structures in Biology

Conference Proceedings

  1. DJ Tobias, SF Sneddon and CL Brooks III. The stability of protein secondary structures in aqueous solution. In AIP Conference Proceedings (Obernai, France).

1990

Journal Article

  1. 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, 112:3307-12.
  1. 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, 30:239-56.  PubMed
  1. SH Fleischman and CL Brooks III. Protein-drug interactions: characterization of inhibitor binding in complexes of DHFR with trimethoprim and related derivatives. Proteins, 1990, 7:52-61.  PubMed
  1. 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, 92:2582-92.
  1. DJ Tobias, SF Sneddon and CL Brooks III. Reverse turns in blocked dipeptides are intrinsically unstable in water. J Mol Biol, 1990, 216:783-96.  PubMed

Book Chapter

  1. CL Brooks III. Molecular simulations of protein structure, dynamics and thermodynamics. In Computer Modeling of Fluids, Polymers and Solids. Edited by C Catlow. Series title: NATO ASI Series, Series C: Mathematical and Physical Sciences. Volume: 293, In Computer Modeling of Fluids, Polymers and Solids

1989

Journal Article

  1. 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, 208:159-81.  PubMed
  1. 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, 93:490-4.
  1. T Head-Gordon, M Head-Gordon, MJ Frisch, CL Brooks III and J Pople. A theoretical study of alanine dipeptide and analogs. International Journal of Quantum Chemistry, Quantum Biology Symposium, 1989, 16:311-22.
  1. SF Sneddon, RS Morgan and CL Brooks III. Toward a model of electronic coupling in proteins. J Phys Chem, 1989, 93:8115-18.
  1. SF Sneddon, DJ Tobias and CL Brooks III. Thermodynamics of amide hydrogen bond formation in polar and apolar solvents. J Mol Biol, 1989, 209:817-20.  PubMed
  1. DJ Tobias, CL Brooks III and SH Fleischman. Conformational flexibility in free energy simulations. J Chem Phys, 1989, 156:256-60.

1988

Journal Article

  1. SF Sneddon and CL Brooks III. The influence of geometrical fluctuations on electron tunneling barriers in proteins. International Journal of Quantum Chemistry, Quantum Biology Symposium, 1988, 15:23-32.
  1. 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, 53:83-9. PMCID: 1330124.  PubMed
  1. DJ Tobias and CL Brooks III. Molecular dynamics with internal coordinate constraints. J Chem Phys, 1988, 89:5115-27.

Book

  1. CL Brooks III, M Karplus and BM Pettitt. Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics. In Advances in Chemical Physics. Edited by I Prigogine, S Rice. Published by John Wiley & Sons (New York). Volume: 71, In Advances in Chemical Physics

Conference Proceedings

  1. CL Brooks III. Thermodynamic calculations on biological molecules. In Computer Simulations of Biomolecular Systems: Theoretical and Experimental Applications (Princeton, N.J.).

1987

Journal Article

  1. CL Brooks III. Scaling behavior of atomic motions: Fractal analysis of particle trajectories. Phys Rev A, 1987, 35:5178-82.
  1. CL Brooks III. The influence of long-range force truncation on the thermodynamics of aqueous ionic solutions. J Chem Phys, 1987, 86:5156-62.
  1. SH Fleischman and CL Brooks III. Thermodynamics of aqueous solvation: solution properties of alcohols and alkanes. J Chem Phys, 1987, 87:3029-37.
  1. 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, 87:5892-4.
  1. T Head-Gordon and CL Brooks III. The role of electrostatics in the binding of small ligands to enzymes. J Phys Chem, 1987, 91:3342-9.
  1. DJ Tobias and CL Brooks III. Calculation of free energy surfaces using the methods of thermodynamic perturbation theory. J Chem Phys, 1987, 142:472-6.

1986

Journal Article

  1. CL Brooks III. Thermodynamics of ionic solvation: Monte Carlo simulations of aqueous chloride and bromide ions. J Phys Chem, 1986, 90:6680-4.
  1. CL Brooks III, A Brunger, M Francl, K Haydock, LC Allen and M Karplus. Role of active site residues and solvation in RNase A. Annals of the New York Academy of Sciences, 1986, 471:295-8.

Book Chapter

  1. CL Brooks III and M Karplus. Theoretical approaches to solvation of biopolymers. In Biomembranes a volume of Methods in Enzymology. Series title: Methods in Enzymology. Published by Academic Press, Inc. (New York). Volume: 127, In Biomembranes a volume of Methods in Enzymology

1985

Journal Article

  1. CL Brooks III, A Brunger and M Karplus. Active site dynamics in protein molecules: a stochastic boundary molecular-dynamics approach. Biopolymers, 1985, 24:843-65.  PubMed
  1. 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, 83:5897-908.
  1. AT Brunger, CL Brooks III and M Karplus. Active site dynamics of ribonuclease. Proc Natl Acad Sci U S A, 1985, 82:8458-62. PMCID: 390935.  PubMed

1984

Journal Article

  1. CL Brooks III and SA Adelman. Dynamics of liquid-state chemical reactions: photolysis of molecular iodine in liquid xenon. J Chem Phys, 1984, 80:5598-609.
  1. A Bruenger, CL Brooks III and M Karplus. Stochastic boundary conditions for molecular dynamics simulations of ST2 water. J Chem Phys, 1984, 105:495-500.
  1. 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. Inorganica Chimica Acta, 1984, 86:13-18.

1983

Journal Article

  1. 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, 79:804-15.
  1. 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, 79:784-803.
  1. CL Brooks III and M Karplus. Deformable stochastic boundaries in molecular dynamics. J Chem Phys, 1983, 79:6312-25.

1982

Journal Article

  1. SA Adelman and CL Brooks III. Generalized Langevin models and condensed-phase chemical reaction dynamics. J Phys Chem, 1982, 86:1511-24.
  1. CL Brooks III and SA Adelman. Dynamics of liquid state chemical reactions: modeling of R-dependent correlation functions. J Chem Phys, 1982, 77:484-97.
  1. 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, 76:1007-23.

1980

Journal Article

  1. M Berkowitz, CL Brooks III and SA Adelman. Generalized Langevin theory for many-body problems in chemical dynamics: modeling of solid and liquid state response functions. J Chem Phys, 1980, 72:3889-98.
  1. 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, 73:4353-64.

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