Publications

2025

Journal Article

  1. BK Chatterjee, M Alam, A Chakravorty, SM Lacy, W Giblin, J Rech, CL Brooks III, P Arvan and MC Truttmann. Small-Molecule FICD Inhibitors Suppress Endogenous and Pathologic FICD-Mediated Protein AMPylation. , 2025, 20:880–895. PMCID: PMC12007993.  PubMed

2024

Journal Article

  1. CL Brooks III, AD MacKerell Jr, CB Post and L Nilsson. Biomolecular dynamics in the 21st century. , 2024, 1868:130534. PMCID: PMC10842176.  PubMed
  1. A Chakravorty, A Hussain, LF Cervantes, TT Lai and CL Brooks III. Exploring the Limits of the Generalized CHARMM and AMBER Force Fields through Predictions of Hydration Free Energy of Small Molecules. , 2024, 64:4089–4101. PMCID: PMC11275216.  PubMed
  1. SE Champagne, CH Chiang, PM Gemmel, CL Brooks III and ARH Narayan. Biocatalytic Stereoselective Oxidation of 2-Arylindoles. , 2024, 146:2728–2735. PMCID: PMC11214688.  PubMed
  1. CH Chiang, Y Wang, A Hussain, CL Brooks III and ARH Narayan. Ancestral Sequence Reconstruction to Enable Biocatalytic Synthesis of Azaphilones. , 2024, 146:30194–30203.  PubMed
  1. P Gartan, F Khorsand, P Mizar, JI Vahokovski, LF Cervantes, BE Haug, R Brenk, CL Brooks III and N Reuter. Investigating Polypharmacology through Targeting Known Human Neutrophil Elastase Inhibitors to Proteinase 3. , 2024, 64:621–626. PMCID: PMC10865350.  PubMed
  1. RL Hayes, LF Cervantes, JC Abad Santos, A Samadi, JZ Vilseck and CL Brooks III. How to Sample Dozens of Substitutions per Site with lambda Dynamics. , 2024, 20:6098–6110. PMCID: PMC11270746.  PubMed
  1. RL Hayes, CF Nixon, S Marqusee and CL Brooks III. Selection pressures on evolution of ribonuclease H explored with rigorous free-energy-based design. , 2024, 121:e2312029121. PMCID: PMC10801872.  PubMed
  1. A Hussain and CL Brooks III. Guiding discovery of protein sequence-structure-function modeling. , 2024, 40.  PMCID: PMC10789314..  PubMed
  1. W Hwang, SL Austin, A Blondel, ED Boittier, S Boresch, M Buck, J Buckner, A Caflisch, HT Chang, X Cheng, YK Choi, JW Chu, MF Crowley, Q Cui, A Damjanovic, Y Deng, M Devereux, X Ding, MF Feig, J Gao, DR Glowacki, JE Gonzales 2nd, MB Hamaneh, ED Harder, RL Hayes, J Huang, Y Huang, PS Hudson, W Im, SM Islam, W Jiang, MR Jones, S Kaser, FL Kearns, NR Kern, JB Klauda, T Lazaridis, J Lee, JA Lemkul, X Liu, Y Luo, AD MacKerell Jr, DT Major, M Meuwly, K Nam, L Nilsson, V Ovchinnikov, E Paci, S Park, RW Pastor, AR Pittman, CB Post, S Prasad, J Pu, Y Qi, T Rathinavelan, DR Roe, B Roux, CN Rowley, J Shen, AC Simmonett, AJ Sodt, K Topfer, M Upadhyay, A van der Vaart, LI Vazquez-Salazar, RM Venable, LC Warrensford, HL Woodcock, Y Wu, CL Brooks III, BR Brooks and M Karplus. CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed. , 2024, 128:9976–10042. PMCID: PMC11492285.  PubMed
  1. TT Lai and CL Brooks III. Accuracy and Reproducibility of Lipari-Szabo Order Parameters From Molecular Dynamics. , 2024, 128:10813–10822. PMCID: PMC11790309.  PubMed
  1. X Liu and CL Brooks III. Enhanced Sampling of Buried Charges in Free Energy Calculations Using Replica Exchange with Charge Tempering. , 2024, 20:1051–1061. PMCID: PMC11275198.  PubMed
  1. J Schimunek, P Seidl, K Elez, T Hempel, T Le, F Noe, S Olsson, L Raich, R Winter, H Gokcan, F Gusev, EM Gutkin, O Isayev, MG Kurnikova, CH Narangoda, R Zubatyuk, IP Bosko, KV Furs, AD Karpenko, YV Kornoushenko, M Shuldau, A Yushkevich, MB Benabderrahmane, P Bousquet-Melou, R Bureau, B Charton, BC Cirou, G Gil, WJ Allen, S Sirimulla, S Watowich, N Antonopoulos, N Epitropakis, A Krasoulis, V Itsikalis, S Theodorakis, I Kozlovskii, A Maliutin, A Medvedev, P Popov, M Zaretckii, H Eghbal-Zadeh, C Halmich, S Hochreiter, A Mayr, P Ruch, M Widrich, F Berenger, A Kumar, Y Yamanishi, KYJ Zhang, E Bengio, Y Bengio, MJ Jain, M Korablyov, CH Liu, G Marcou, E Glaab, K Barnsley, SM Iyengar, MJ Ondrechen, VJ Haupt, F Kaiser, M Schroeder, L Pugliese, S Albani, C Athanasiou, A Beccari, P Carloni, G D'Arrigo, E Gianquinto, J Gossen, A Hanke, BP Joseph, DB Kokh, S Kovachka, C Manelfi, G Mukherjee, A Muniz-Chicharro, F Musiani, A Nunes-Alves, G Paiardi, G Rossetti, SK Sadiq, F Spyrakis, C Talarico, A Tsengenes, RC Wade, C Copeland, J Gaiser, DR Olson, A Roy, V Venkatraman, TJ Wheeler, H Arthanari, K Blaschitz, M Cespugli, V Durmaz, K Fackeldey, PD Fischer, C Gorgulla, C Gruber, K Gruber, M Hetmann, JE Kinney, KM Padmanabha Das, S Pandita, A Singh, G Steinkellner, G Tesseyre, G Wagner, ZF Wang, RJ Yust, DS Druzhilovskiy, DA Filimonov, PV Pogodin, V Poroikov, AV Rudik, LA Stolbov, AV Veselovsky, M De Rosa, G De Simone, MR Gulotta, J Lombino, N Mekni, U Perricone, A Casini, A Embree, DB Gordon, D Lei, K Pratt, CA Voigt, KY Chen, Y Jacob, T Krischuns, P Lafaye, A Zettor, ML Rodriguez, KM White, D Fearon, F Von Delft, MA Walsh, D Horvath, CL Brooks III, B Falsafi, B Ford, A Garcia-Sastre, S Yup Lee, N Naffakh, A Varnek, G Klambauer and TM Hermans. A community effort in SARS-CoV-2 drug discovery. , 2024, 43:e202300262. PMCID: PMC11299051.  PubMed
  1. Y Wu, F Liu, I Glenn, K Fonseca-Valencia, L Paris, Y Xiong, SV Jerome, CL Brooks III and BK Shoichet. Identifying Artifacts from Large Library Docking. , 2024, 67:16796–16806. PMCID: PMC11890070.  PubMed
  1. D Yang, CH Chiang, T Wititsuwannakul, CL Brooks III, PM Zimmerman and ARH Narayan. Engineering the Reaction Pathway of a Non-heme Iron Oxygenase Using Ancestral Sequence Reconstruction. , 2024, 146:34352–34363.  PubMed

2023

Journal Article

  1. F Ahmed and CL Brooks III. FASTDock: A Pipeline for Allosteric Drug Discovery. , 2023, 63:7219–7227. PMCID: PMC10773972.  PubMed
  1. J Buckner, X Liu, A Chakravorty, Y Wu, LF Cervantes, TT Lai and CL Brooks III. pyCHARMM: Embedding CHARMM Functionality in a Python Framework. , 2023, 19:3752–3762. PMCID: PMC10504603.  PubMed
  1. CH Chiang, T Wymore, A Rodriguez Benitez, A Hussain, JL Smith, CL Brooks III and ARH Narayan. Deciphering the evolution of flavin-dependent monooxygenase stereoselectivity using ancestral sequence reconstruction. , 2023, 120:e2218248120. PMCID: PMC10104550.  PubMed
  1. X Liu, PK Tsang, MB Soellner and CL Brooks III. QSAR via multisite lambda-dynamics in the orphaned TSSK1B kinase. , 2023, 32:e4623. PMCID: PMC10031809.  PubMed
  1. AL Peiffer, JM Garlick, Y Wu, JW Wotring, S Arora, AS Harmata, DA Bochar, CJ Stephenson, MB Soellner, JZ Sexton, CL Brooks III and AK Mapp. TMPRSS2 Inhibitor Discovery Facilitated through an In Silico and Biochemical Screening Platform. , 2023, 14:860–866. PMCID: PMC10237299.  PubMed

2022

Journal Article

  1. A Chakravorty, SD McCalpin, BR Sahoo, A Ramamoorthy and CL Brooks III. Free Gangliosides Can Alter Amyloid-beta Aggregation. , 2022, 13:9303–9308. PMCID: PMC9700483.  PubMed
  1. EE Guest, LF Cervantes, SD Pickett, CL Brooks III and JD Hirst. Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4. , 2022, 62:1458–1470. PMCID: PMC9098113.  PubMed
  1. RL Hayes, JZ Vilseck and CL Brooks III. Addressing Intersite Coupling Unlocks Large Combinatorial Chemical Spaces for Alchemical Free Energy Methods. , 2022, 18:2114–2123. PMCID: PMC9700482.  PubMed
  1. DWS MacKenzie, A Schaefer, J Steckner, CA Leo, D Naser, E Artikis, A Broom, T Ko, P Shah, MQ Ney, E Tran, MTJ Smith, B Fuglestad, AJ Wand, CL Brooks III and EM Meiering. A fine balance of hydrophobic-electrostatic communication pathways in a pH-switching protein. , 2022, 119:e2119686119. PMCID: PMC9245636.  PubMed
  1. AL Peiffer, JM Garlick, ST Joy, AK Mapp and CL Brooks III. Allostery in the dynamic coactivator domain KIX occurs through minor conformational micro-states. , 2022, 18:e1009977. PMCID: PMC9067669.  PubMed
  1. JZ Vilseck, LF Cervantes, RL Hayes and CL Brooks III. Optimizing Multisite lambda-Dynamics Throughput with Charge Renormalization. , 2022, 62:1479–1488. PMCID: PMC9700484.  PubMed
  1. Y Wu and CL Brooks III. Covalent docking in CDOCKER. , 2022, 36:563–574. PMCID: PMC9700487.  PubMed

2021

Journal Article

  1. CL Brooks III, DA Case, S Plimpton, B Roux, D van der Spoel and E Tajkhorshid. Classical molecular dynamics. , 2021, 154:100401.  PubMed
  1. JM Garlick, SM Sturlis, PA Bruno, JA Yates, AL Peiffer, Y Liu, L Goo, L Bao, SN De Salle, G Tamayo-Castillo, CL Brooks III, SD Merajver and AK Mapp. Norstictic Acid Is a Selective Allosteric Transcriptional Regulator. , 2021, 143:9297–9302. PMCID: PMC8717358.  PubMed
  1. RL Hayes and CL Brooks III. A strategy for proline and glycine mutations to proteins with alchemical free energy calculations. , 2021, 42:1088–1094. PMCID: PMC8628859.  PubMed
  1. RL Hayes, J Buckner and CL Brooks III. BLaDE: A Basic Lambda Dynamics Engine for GPU-Accelerated Molecular Dynamics Free Energy Calculations. , 2021, 17:6799–6807. PMCID: PMC8626863.  PubMed
  1. JZ Vilseck, X Ding, RL Hayes and CL Brooks III. Generalizing the Discrete Gibbs Sampler-Based lambda-Dynamics Approach for Multisite Sampling of Many Ligands. , 2021, 17:3895–3907. PMCID: PMC8627277.  PubMed
  1. Q Wan, BC Bennett, T Wymore, Z Li, MA Wilson, CL Brooks III, P Langan, A Kovalevsky and CG Dealwis. Capturing the Catalytic Proton of Dihydrofolate Reductase: Implications for General Acid-Base Catalysis. , 2021, 11:5873–5884. PMCID: PMC8154319.  PubMed
  1. Y Wu and CL Brooks III. Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy. , 2021, 61:5535–5549. PMCID: PMC8684595.  PubMed

2020

Journal Article

  1. X Ding, Y Wu, Y Wang, JZ Vilseck and CL Brooks III. Accelerated CDOCKER with GPUs, Parallel Simulated Annealing, and Fast Fourier Transforms. , 2020, 16:3910–3919. PMCID: PMC7076882.  PubMed
  1. X Gong, M Chiricotto, X Liu, E Nordquist, M Feig, CL Brooks III and J Chen. Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units. , 2020, 41:830–838. PMCID: PMC7076882.  PubMed
  1. TJ Paul, JZ Vilseck, RL Hayes and CL Brooks III. Exploring pH Dependent Host/Guest Binding Affinities. , 2020, 124:6520–6528. PMCID: PMC7442968.  PubMed
  1. EP Raman, TJ Paul, RL Hayes and CL Brooks III. Automated, Accurate, and Scalable Relative Protein-Ligand Binding Free-Energy Calculations Using Lambda Dynamics. , 2020, 16:7895–7914. PMCID: PMC7814773.  PubMed
  1. H Torabifard, A Panahi and CL Brooks III. M2 amphipathic helices facilitate pH-dependent conformational transition in influenza A virus. , 2020, 117:3583–3591. PMCID: PMC7035486.  PubMed
  1. Y Wang and CL Brooks III. Electrostatic Forces Control the Negative Allosteric Regulation in a Disordered Protein Switch. , 2020, 11:864–868.  PubMed

2019

Journal Article

  1. E Artikis and CL Brooks III. Modeling pH-Dependent NMR Chemical Shift Perturbations in Peptides. , 2019, 117:258–268. PMCID: PMC6700603.  PubMed
  1. AR Benitez, S Tweedy, SA Baker Dockrey, AL Lukowski, T Wymore, D Khare, CL Brooks III, BA Palfey, JL Smith and ARH Narayan. Structural basis for selectivity in flavin-dependent monooxygenase-catalyzed oxidative dearomatization. , 2019, 9:3633–3640. PMCID: PMC6658140.  PubMed
  1. H Deng, S Ke, R Callender, G Balakrishnan, TG Spiro, ER May and CL Brooks III. Computational Studies of Catalytic Loop Dynamics in Yersinia Protein Tyrosine Phosphatase Using Pathway Optimization Methods. , 2019, 123:7840–7851. PMCID: PMC6752976.  PubMed
  1. X Ding, JZ Vilseck and CL Brooks III. Fast Solver for Large Scale Multistate Bennett Acceptance Ratio Equations. , 2019, 15:799–802. PMCID: PMC6372332.  PubMed
  1. X Ding, Z Zou and C Brooks III. Deciphering protein evolution and fitness landscapes with latent space models. , 2019, 10:5644. PMCID: PMC6904478.  PubMed
  1. SAB Dockrey, CE Suh, AR Benitez, T Wymore, CL Brooks III and ARH Narayan. Positioning-Group-Enabled Biocatalytic Oxidative Dearomatization. , 2019, 5:1010–1016. PMCID: PMC6598382.  PubMed
  1. KT Halloran, Y Wang, K Arora, S Chakravarthy, TC Irving, O Bilsel, CL Brooks III and CR Matthews. Frustration and folding of a TIM barrel protein. , 2019, 116:16378–16383. PMCID: PMC6697809.  PubMed
  1. SE Tweedy, A Rodriguez Benitez, ARH Narayan, PM Zimmerman, CL Brooks III and T Wymore. Hydroxyl Radical-Coupled Electron-Transfer Mechanism of Flavin-Dependent Hydroxylases. , 2019, 123:8065–8073. PMCID: PMC6943927.  PubMed
  1. JZ Vilseck, N Sohail, RL Hayes and CL Brooks III. Overcoming Challenging Substituent Perturbations with Multisite lambda-Dynamics: A Case Study Targeting beta-Secretase 1. , 2019, 10:4875–4880. PMCID: PMC7015761.  PubMed
  1. Y Wang and CL Brooks III. Enhanced Sampling Applied to Modeling Allosteric Regulation in Transcription. , 2019, 10:5963–5968.  PubMed
  1. M Xiao, S Wei, J Chen, J Tian, CL Brooks III, ENG Marsh and Z Chen. Molecular Mechanisms of Interactions between Monolayered Transition Metal Dichalcogenides and Biological Molecules. , 2019, 141:9980–9988.  PubMed

2018

Journal Article

  1. X Ding, RL Hayes, JZ Vilseck, MK Charles and CL Brooks III. CDOCKER and lambda-dynamics for prospective prediction in D(3)R Grand Challenge 2. , 2018, 32:89–102. PMCID: PMC5767529.  PubMed
  1. RL Hayes, JZ Vilseck and CL Brooks III. Approaching protein design with multisite lambda dynamics: Accurate and scalable mutational folding free energies in T4 lysozyme. , 2018, 27:1910–1922. PMCID: PMC6225981.  PubMed
  1. AR Henderson, MJ Henley, NJ Foster, AL Peiffer, MS Beyersdorf, KD Stanford, SM Sturlis, BM Linhares, ZB Hill, JA Wells, T Cierpicki, CL Brooks III, CA Fierke and AK Mapp. Conservation of coactivator engagement mechanism enables small-molecule allosteric modulators. , 2018, 115:8960–8965. PMCID: PMC6130367.  PubMed
  1. PT Ho, DJ Montiel-Garcia, JJ Wong, M Carrillo-Tripp, CL Brooks III, JE Johnson and VS Reddy. VIPERdb: A Tool for Virus Research. , 2018, 5:477–488.  PubMed
  1. S Horowitz, L Salmon, P Koldewey, LS Ahlstrom, R Martin, S Quan, PV Afonine, H van den Bedem, L Wang, Q Xu, RC Trievel, CL Brooks III and JCA Bardwell. Reply to 'Misreading chaperone-substrate complexes from random noise'. , 2018, 25:990–991.  PubMed
  1. Y Li, TL Ogorzalek, S Wei, X Zhang, P Yang, J Jasensky, CL Brooks III, ENG Marsh and Z Chen. Effect of immobilization site on the orientation and activity of surface-tethered enzymes. , 2018, 20:1021–1029.  PubMed
  1. JZ Vilseck, KA Armacost, RL Hayes, GB Goh and CL Brooks III. Predicting Binding Free Energies in a Large Combinatorial Chemical Space Using Multisite λ-Dynamics. , 2018, 9:3328–3332. PMCID: PMC6091208.  PubMed
  1. JR Widom, YA Nedialkov, V Rai, RL Hayes, CL Brooks III, I Artsimovitch and NG Walter. Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing. , 2018, 72:541–552 e6.  PubMed
  1. M Xiao, S Wei, Y Li, J Jasensky, J Chen, CL Brooks III and Z Chen. Molecular interactions between single layered MoS2 and biological molecules. , 2018, 9:1769–1773. PMCID: PMC5885976.  PubMed
  1. X Zou, S Wei, S Badieyan, M Schroeder, J Jasensky, CL Brooks III, ENG Marsh and Z Chen. Investigating the Effect of Two-Point Surface Attachment on Enzyme Stability and Activity. , 2018, 140:16560–16569.  PubMed

2017

Journal Article

  1. M Daher, AM Mustoe, A Morriss-Andrews, CL Brooks III and NG Walter. Tuning RNA folding and function through rational design of junction topology. , 2017, 45:9706–9715. PMCID: PMC5766210.  PubMed
  1. X Ding, JZ Vilseck, RL Hayes and CL Brooks III. Gibbs Sampler-Based lambda-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation. , 2017, 13:2501–2510.  PubMed
  1. RL Hayes, KA Armacost, JZ Vilseck and CL Brooks III. Adaptive Landscape Flattening Accelerates Sampling of Alchemical Space in Multisite lambda Dynamics. , 2017, 121:3626–3635. PMCID: PMC5824625.  PubMed
  1. K Kamgar-Parsi, L Hong, A Naito, CL Brooks III and A Ramamoorthy. Growth-incompetent monomers of human calcitonin lead to a noncanonical direct relationship between peptide concentration and aggregation lag time. , 2017, 292:14963–14976. PMCID: PMC5592673.  PubMed
  1. S Kim, J Lee, S Jo, CL Brooks III, HS Lee and W Im. CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules. , 2017, 38:1879–1886. PMCID: PMC5488718.  PubMed
  1. M Su, EZ Guo, X Ding, Y Li, JT Tarrasch, CL Brooks III, Z Xu and G Skiniotis. Mechanism of Vps4 hexamer function revealed by cryo-EM. , 2017, 3:e1700325. PMCID: PMC5392032.  PubMed
  1. S Wei, LS Ahlstrom and CL Brooks III. Exploring Protein-Nanoparticle Interactions with Coarse-Grained Protein Folding Models. , 2017, 13:1603748. PMCID: PMC5551056.  PubMed
  1. S Wei, CL Brooks III and AT Frank. A rapid solvent accessible surface area estimator for coarse grained molecular simulations. , 2017, 38:1270–1274.  PubMed
  1. X Zou, S Wei, J Jasensky, M Xiao, Q Wang, CL Brooks III and Z Chen. Molecular Interactions between Graphene and Biological Molecules. , 2017, 139:1928–1936.  PubMed

2016

Journal Article

  1. A Aggarwal, ER May, CL Brooks III and WS Klug. Nonuniform elastic properties of macromolecules and effect of prestrain on their continuum nature. , 2016, 93:012417.  PubMed
  1. EJ Arthur and CL Brooks III. Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors. , 2016, 37:927–39. PMCID: PMC4801733.  PubMed
  1. EJ Arthur and CL Brooks III. Efficient implementation of constant pH molecular dynamics on modern graphics processors. , 2016, 37:2171–80. PMCID: PMC4981528.  PubMed
  1. PA Bruno, A Morriss-Andrews, AR Henderson, CL Brooks III and AK Mapp. A Synthetic Loop Replacement Peptide That Blocks Canonical NF-kappaB Signaling. , 2016, 55:14997–15001. PMCID: PMC5587901.  PubMed
  1. A Dickson, LS Ahlstrom and CL Brooks III. Coupled folding and binding with 2D Window-Exchange Umbrella Sampling. , 2016, 37:587–94. PMCID: PMC4744578.  PubMed
  1. JK Gagnon, SM Law and CL Brooks III. Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM. , 2016, 37:753–62. PMCID: PMC4776757.  PubMed
  1. S Horowitz, L Salmon, P Koldewey, LS Ahlstrom, R Martin, S Quan, PV Afonine, H van den Bedem, L Wang, Q Xu, RC Trievel, CL Brooks III and JC Bardwell. Visualizing chaperone-assisted protein folding. , 2016, 23:691–7. PMCID: PMC4937829.  PubMed
  1. J Lee, X Cheng, JM Swails, MS Yeom, PK Eastman, JA Lemkul, S Wei, J Buckner, JC Jeong, Y Qi, S Jo, VS Pande, DA Case, CL Brooks III, AD MacKerell Jr, JB Klauda and W Im. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. , 2016, 12:405–13. PMCID: PMC4712441.  PubMed
  1. AM Mustoe, HM Al-Hashimi and CL Brooks III. Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme. , 2016, 44:402–12. PMCID: PMC4705646.  PubMed
  1. CB Post and CL Brooks III. Editorial. , 2016, 25:5–8. PMCID: PMC4815299.  PubMed
  1. L Salmon, LS Ahlstrom, S Horowitz, A Dickson, CL Brooks III and JC Bardwell. Capturing a Dynamic Chaperone-Substrate Interaction Using NMR-Informed Molecular Modeling. , 2016, 138:9826–39. PMCID: PMC5242313.  PubMed
  1. I Soteras Gutierrez, FY Lin, K Vanommeslaeghe, JA Lemkul, KA Armacost, CL Brooks III and AD MacKerell Jr. Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand-protein interactions. , 2016, 24:4812–4825. PMCID: PMC5053860.  PubMed
  1. SJ Won, D Davda, KJ Labby, SY Hwang, R Pricer, JD Majmudar, KA Armacost, LA Rodriguez, CL Rodriguez, FS Chong, KA Torossian, J Palakurthi, ES Hur, JL Meagher, CL Brooks III, JA Stuckey and BR Martin. Molecular Mechanism for Isoform-Selective Inhibition of Acyl Protein Thioesterases 1 and 2 (APT1 and APT2). , 2016, 11:3374–3382. PMCID: PMC5359770.  PubMed

2015

Journal Article

  1. LS Ahlstrom, SM Law, A Dickson and CL Brooks III. Multiscale Modeling of a Conditionally Disordered pH-Sensing Chaperone. , 2015, 427:1670–80. PMCID: PMC4380812.  PubMed
  1. KA Armacost, GB Goh and CL Brooks III. Biasing Potential Replica Exchange Multisite lambda-Dynamics for Efficient Free Energy Calculations. , 2015, 11:1267–77. PMCID: PMC4731093.  PubMed
  1. M Carrillo-Tripp, DJ Montiel-Garcia, CL Brooks III and VS Reddy. CapsidMaps: Protein-protein interaction pattern discovery platform for the structural analysis of virus capsids using Google Maps. , 2015, 190:47–55.  PubMed
  1. S Cheng and CL Brooks III. Protein-Protein Interfaces in Viral Capsids Are Structurally Unique. , 2015, 427:3613–24. PMCID: PMC4624513.  PubMed
  1. S Cheng, Y Zhang and CL Brooks III. PCalign: a method to quantify physicochemical similarity of protein-protein interfaces. , 2015, 16:33. PMCID: PMC4339745.  PubMed
  1. B Ding, A Panahi, JJ Ho, JE Laaser, CL Brooks III, MT Zanni and Z Chen. Probing Site-Specific Structural Information of Peptides at Model Membrane Interface In Situ. , 2015, 137:10190–8.  PubMed
  1. AT Frank, SM Law, LS Ahlstrom and CL Brooks III. Predicting Protein Backbone Chemical Shifts From Calpha Coordinates: Extracting High Resolution Experimental Observables from Low Resolution Models. , 2015, 11:325–331. PMCID: PMC4295808.  PubMed
  1. GB Goh, DM Eike, BP Murch and CL Brooks III. Accurate modeling of ionic surfactants at high concentration. , 2015, 119:6217–24.  PubMed
  1. EN Laricheva, GB Goh, A Dickson and CL Brooks III. pH-Dependent Transient Conformational States Control Optical Properties in Cyan Fluorescent Protein. , 2015, 137:2892–900. PMCID: PMC4394632.  PubMed
  1. Y Li, S Wei, J Wu, J Jasensky, C Xi, H Li, Y Xu, Q Wang, EN Marsh, CL Brooks III and Z Chen. Effects of Peptide Immobilization Sites on the Structure and Activity of Surface-Tethered Antimicrobial Peptides. , 2015, 119:7146–55.
  1. AM Mustoe, X Liu, PJ Lin, HM Al-Hashimi, CA Fierke and CL Brooks III. Noncanonical Secondary Structure Stabilizes Mitochondrial tRNA(Ser(UCN)) by Reducing the Entropic Cost of Tertiary Folding. , 2015, 137:3592–9. PMCID: PMC4399864.  PubMed
  1. TL Ogorzalek, S Wei, Y Liu, Q Wang, CL Brooks III, Z Chen and EN Marsh. Molecular-Level Insights into Orientation-Dependent Changes in the Thermal Stability of Enzymes Covalently Immobilized on Surfaces. , 2015, 31:6145–53.  PubMed
  1. A Panahi and CL Brooks III. Membrane Environment Modulates the pKa Values of Transmembrane Helices. , 2015, 119:4601–7. PMCID: PMC4404502.  PubMed
  1. QM Wang, S Wei, JF Wu, XQ Zou, O Sieggreen, YW Liu, CW Xi, CL Brooks III and Z Chen. Interfacial Behaviors of Antimicrobial Peptide Cecropin P1 Immobilized on Different Self-Assembled Monolayers. , 2015, 119:22542–22551.
  1. S Wei and CL Brooks III. Stability and orientation of cecropin P1 on maleimide self-assembled monolayer (SAM) surfaces and suggested functional mutations. , 2015, 26:485–490.
  1. SJ Wijeyesakere, JK Gagnon, K Arora, CL Brooks III and M Raghavan. Regulation of calreticulin-major histocompatibility complex (MHC) class I interactions by ATP. , 2015, 112:E5608–17. PMCID: PMC4611598.  PubMed
  1. JD Yesselman, S Horowitz, CL Brooks III and RC Trievel. Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures. , 2015, 83:403–10. PMCID: PMC4747036.  PubMed
  1. X Zeng, S Mukhopadhyay and CL Brooks III. Residue-level resolution of alphavirus envelope protein interactions in pH-dependent fusion. , 2015, 112:2034–9. PMCID: PMC4343099.  PubMed

2014

Journal Article

  1. EJ Arthur, JT King, KJ Kubarych and CL Brooks III. Heterogeneous preferential solvation of water and trifluoroethanol in homologous lysozymes. , 2014, 118:8118–27. PMCID: 4216199.  PubMed
  1. A Dickson and CL Brooks III. WExplore: Hierarchical Exploration of High-Dimensional Spaces Using the Weighted Ensemble Algorithm. , 2014, 118:3532–42. PMCID: PMC24490961.  PubMed
  1. A Dickson, AM Mustoe, L Salmon and CL Brooks III. Efficient in silico exploration of RNA interhelical conformations using Euler angles and WExplore. , 2014, 42:12126–37. PMCID: PMC4231733.  PubMed
  1. AT Frank, SM Law and CL Brooks III. A simple and fast approach for predicting (1)h and (13)c chemical shifts: toward chemical shift-guided simulations of RNA. , 2014, 118:12168–75. PMCID: PMC4207130.  PubMed
  1. GB Goh, BS Hulbert, H Zhou and CL Brooks III. Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism. , 2014, 82:1319–31. PMCID: PMC4394622.  PubMed
  1. GB Goh, EN Laricheva and CL Brooks III. Uncovering pH-dependent transient states of proteins with buried ionizable residues. , 2014, 136:8496–9. PMCID: PMC4227812.  PubMed
  1. X Han, Y Liu, FG Wu, J Jasensky, T Kim, Z Wang, CL Brooks III, J Wu, C Xi, CM Mello and Z Chen. Different interfacial behaviors of peptides chemically immobilized on surfaces with different linker lengths and via different termini. , 2014, 118:2904–12.  PubMed
  1. JT King, EJ Arthur, CL Brooks III and KJ Kubarych. Crowding Induced Collective Hydration of Biological Macromolecules over Extended Distances. , 2014, 136:188–94. PMCID: 3983708.  PubMed
  1. SM Law, LS Ahlstrom, A Panahi and CL Brooks III. Hamiltonian Mapping Revisited: Calibrating Minimalist Models to Capture Molecular Recognition by Intrinsically Disordered Proteins. , 2014, 5:3441–3444. PMCID: PMC4183358.  PubMed
  1. SM Law, AT Frank and CL Brooks III. PCASSO: A fast and efficient Calpha-based method for accurately assigning protein secondary structure elements. , 2014, 35:1757–61. PMCID: PMC4127665.  PubMed
  1. SM Law, JK Gagnon, AK Mapp and CL Brooks III. Prepaying the entropic cost for allosteric regulation in KIX. , 2014, 111:12067–72. PMCID: PMC4143015.  PubMed
  1. ER May, K Arora and CL Brooks III. pH-Induced Stability Switching of the Bacteriophage HK97 Maturation Pathway. , 2014, 136:3097–3107. PMCID: PMC3985869.  PubMed
  1. AM Mustoe, HM Al-Hashimi and CL Brooks III. Coarse Grained Models Reveal Essential Contributions of Topological Constraints to the Conformational Free Energy of RNA Bulges. , 2014, 118:2615–2627. PMCID: PMC3983386.  PubMed
  1. AM Mustoe, CL Brooks III and HM Al-Hashimi. Hierarchy of RNA functional dynamics. , 2014, 83:441–66. PMCID: PMC4048628.  PubMed
  1. AM Mustoe, CL Brooks III and HM Al-Hashimi. Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity. , 2014, 42:11792–804. PMCID: PMC4191394.  PubMed
  1. RP Nobrega, K Arora, SV Kathuria, R Graceffa, RA Barrea, L Guo, S Chakravarthy, O Bilsel, TC Irving, CL Brooks III and CR Matthews. Modulation of frustration in folding by sequence permutation. , 2014, 111:10562–7. PMCID: PMC4115504.  PubMed
  1. KA Taylor, M Feig, CL Brooks III, PM Fagnant, S Lowey and KM Trybus. Role of the essential light chain in the activation of smooth muscle myosin by regulatory light chain phosphorylation. , 2014, 185:375–82. PMCID: PMC4065857.  PubMed
  1. H Vashisth, G Skiniotis and CL Brooks III. Collective Variable Approaches for Single Molecule Flexible Fitting and Enhanced Sampling. , 2014, 114:3353–3365. PMCID: PMC3983124.  PubMed
  1. Z Wang, X Han, N He, Z Chen and CL Brooks III. Molecular Structures of C- and N-Terminus Cysteine Modified Cecropin P1 Chemically Immobilized onto Maleimide-Terminated Self-Assembled Monolayers Investigated by Molecular Dynamics Simulation. , 2014, 118:5670–80.  PubMed
  1. Z Wang, X Han, N He, Z Chen and CL Brooks III. Environmental effect on surface immobilized biological molecules. , 2014, 118:12176–85.  PubMed
  1. Z Wang, X Han, N He, Z Chen and CL Brooks III. Molecular structures of C- and N-terminus cysteine modified cecropin P1 chemically immobilized onto maleimide-terminated self-assembled monolayers investigated by molecular dynamics simulation. , 2014, 118:5670–80.  PubMed
  1. X Zeng, J Chugh, A Casiano-Negroni, HM Al-Hashimi and CL Brooks III. Flipping of the Ribosomal A-Site Adenines Provides a Basis for tRNA Selection. , 2014, 426:3201–13. PMCID: PMC4150856.  PubMed

2013

Journal Article

  1. LS Ahlstrom, A Dickson and CL Brooks III. Binding and Folding of the Small Bacterial Chaperone HdeA. , 2013, 117:13219–25. PMCID: 3808462.  PubMed
  1. K Arora and CL Brooks III. Multiple intermediates, diverse conformations, and cooperative conformational changes underlie the catalytic hydride transfer reaction of dihydrofolate reductase. , 2013, 337:165–87.  PubMed
  1. CL Brooks III, M Ehara, G Frenking and PR Schreiner. New paint and a new engine. , 2013, 34:1.  PubMed
  1. S Cheng and CL Brooks III. Viral capsid proteins are segregated in structural fold space. , 2013, 9:e1002905. PMCID: PMC3567143.  PubMed
  1. A Dickson and CL Brooks III. Native States of fast-folding proteins are kinetic traps. , 2013, 135:4729–34. PMCID: 3619186.  PubMed
  1. A Dickson and CL Brooks III. Quantifying Chaperone-Mediated Transitions in the Proteostasis Network of E. coli. , 2013, 9:e1003324. PMCID: 3828153.  PubMed
  1. L Foit, JS George, BW Zhang, CL Brooks III and JC Bardwell. Chaperone activation by unfolding. , 2013, 110:E1254–62. PMCID: PMC3619340.  PubMed
  1. GB Goh, JL Knight and CL Brooks III. Towards Accurate Prediction of Protonation Equilibrium of Nucleic Acids. , 2013, 4:760–766. PMCID: PMC3601767.  PubMed
  1. GB Goh, JL Knight and CL Brooks III. pH-dependent dynamics of complex RNA macromolecules. , 2013, 9:935–943. PMCID: PMC3601751.  PubMed
  1. JL Knight, JD Yesselman and CL Brooks III. Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes. , 2013, 34:893–903. PMCID: PMC4402937.  PubMed
  1. EN Laricheva, K Arora, JL Knight and CL Brooks III. Deconstructing activation events in rhodopsin. , 2013, 135:10906–9. PMCID: PMC3774788.  PubMed
  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. , 2013, 22:595–604. PMCID: PMC3649261.  PubMed
  1. EN Nikolova, GB Goh, CL Brooks III and HM Al-Hashimi. Characterizing the protonation state of cytosine in transient G.C Hoogsteen base pairs in duplex DNA. , 2013, 135:6766–9. PMCID: PMC3713198.  PubMed
  1. KC Suddala, AJ Rinaldi, J Feng, AM Mustoe, CD Eichhorn, JA Liberman, JE Wedekind, HM Al-Hashimi, CL Brooks III and NG Walter. Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure. , 2013, 41:10462–75. PMCID: PMC3905878.  PubMed
  1. H Vashisth, G Skiniotis and CL Brooks III. Enhanced sampling and overfitting analyses in structural refinement of nucleic acids into electron microscopy maps. , 2013, 117:3738–46. PMCID: PMC3690198.  PubMed
  1. H Vashisth, AJ Storaska, RR Neubig and CL Brooks III. Conformational dynamics of a regulator of g-protein signaling protein reveals a mechanism of allosteric inhibition by a small molecule. , 2013, 8:2778–84. PMCID: PMC3876963.  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. , 2013, 135:3363–6. PMCID: PMC3607081.  PubMed

2012

Journal Article

  1. A Dickson and CL Brooks III. Quantifying hub-like behavior in protein folding networks. , 2012, 8:3044–3052. PMCID: 3767461.  PubMed
  1. GB Goh, JL Knight and CL Brooks III. Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent. , 2012, 8:36–46. PMCID: PMC3277849.  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. , 2012, 134:15357–70. PMCID: PMC3446636.  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. , 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. , 2012, 51:11258–62. PMCID: PMC3711073.  PubMed
  1. RV Mannige, CL Brooks III and EI Shakhnovich. A universal trend among proteomes indicates an oily last common ancestor. , 2012, 8:e1002839. PMCID: PMC3531291.  PubMed
  1. ER May and CL Brooks III. On the morphology of viral capsids: elastic properties and buckling transitions. , 2012, 116:8604–9. PMCID: PMC3395760.  PubMed
  1. ER May, J Feng and CL Brooks III. Exploring the symmetry and mechanism of virus capsid maturation via an ensemble of pathways. , 2012, 102:606–12. PMCID: PMC3274788.  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. , 2012, 40:892–904. PMCID: PMC3258142.  PubMed
  1. WH Roos, I Gertsman, ER May, CL Brooks III, JE Johnson and GJ Wuite. Mechanics of bacteriophage maturation. , 2012, 109:2342–7. PMCID: PMC3289345.  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. , 2012, 3:3379–3384. PMCID: PMC3505029.  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. , 2012, 20:1453–62. PMCID: PMC3438525.  PubMed
  1. T Wymore and CL Brooks III. From Molecular Phylogenetics to Quantum Chemistry: Discovering Enzyme Design Principles through Computation. , 2012, 2:e201209018. PMCID: PMC3962182.  PubMed
  1. JD Yesselman, DJ Price, JL Knight and CL Brooks III. MATCH: an atom-typing toolset for molecular mechanics force fields. , 2012, 33:189–202. PMCID: PMC3228871.  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. , 2011, 79:3276–86. PMCID: PMC3213318.  PubMed
  1. MH Bailor, AM Mustoe, CL Brooks III and HM Al-Hashimi. 3D maps of RNA interhelical junctions. , 2011, 6:1536–45.  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. , 2011, 21:296–305. PMCID: PMC3319143.  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. , 2011, 40:1345–55. PMCID: PMC3273816.  PubMed
  1. J Feng, NG Walter and CL Brooks III. Cooperative and directional folding of the preQ1 riboswitch aptamer domain. , 2011, 133:4196–9. PMCID: PMC3109358.  PubMed
  1. GB Goh, EB Garcia-Moreno and CL Brooks III. The high dielectric constant of staphylococcal nuclease is encoded in its structural architecture. , 2011, 133:20072–5. PMCID: PMC3241862.  PubMed
  1. JL Knight and CL Brooks III. Surveying implicit solvent models for estimating small molecule absolute hydration free energies. , 2011, 32:2909–23. PMCID: PMC3142295.  PubMed
  1. JL Knight and CL Brooks III. Applying efficient implicit nongeometric constraints in alchemical free energy simulations. , 2011, 32:3423–32. PMCID: PMC3196384.  PubMed
  1. JL Knight and CL Brooks III. Multi-Site lambda-dynamics for simulated Structure-Activity Relationship studies. , 2011, 7:2728–2739. PMCID: PMC3223982.  PubMed
  1. V Lopez-Mejias, JL Knight, CL Brooks III and AJ Matzger. On the mechanism of crystalline polymorph selection by polymer heteronuclei. , 2011, 27:7575–9. PMCID: PMC3124555.  PubMed
  1. ER May, A Aggarwal, WS Klug and CL Brooks III. Viral capsid equilibrium dynamics reveals nonuniform elastic properties. , 2011, 100:L59–61. PMCID: PMC3117158.  PubMed
  1. ER May and CL Brooks III. Determination of viral capsid elastic properties from equilibrium thermal fluctuations. , 2011, 106:188101.  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. , 2011, 51:2047–65. PMCID: PMC3183351.  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. , 2011, 333:1449–53. PMCID: PMC3402165.  PubMed
  1. T Wymore, BY Chen, HB Nicholas Jr, AJ Ropelewski and CL Brooks III. A Mechanism for Evolving Novel Plant Sesquiterpene Synthase Function. , 2011, 30:896–906.  PubMed
  1. BW Zhang, L Brunetti and CL Brooks III. Probing pH-dependent dissociation of HdeA dimers. , 2011, 133:19393–8. PMCID: PMC3227773.  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. , 2010, 78:1926–38. PMCID: PMC4442682.  PubMed
  1. DL Bostick and CL Brooks III. Selective complexation of K+ and Na+ in simple polarizable ion-ligating systems. , 2010, 132:13185–7. PMCID: PMC3051181.  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. , 2010, 398:332–50. PMCID: PMC2862464.  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. , 2010, 114:16263–72. PMCID: PMC3005859.  PubMed
  1. RV Mannige and CL Brooks III. Periodic table of virus capsids: implications for natural selection and design. , 2010, 5:e9423. PMCID: PMC2831995.  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. , 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. , 2010, 78:2189–201. PMCID: PMC2933064.  PubMed
  1. K Yoshimoto, K Arora and CL Brooks III. Hexameric helicase deconstructed: interplay of conformational changes and substrate coupling. , 2010, 98:1449–57. PMCID: PMC2856183.  PubMed
  1. J Zimmermann, FE Romesberg, CL Brooks III and IF Thorpe. Molecular description of flexibility in an antibody combining site. , 2010, 114:7359–70. PMCID: PMC2892760.  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. , 2009, 5:2909–2923. PMCID: PMC2772076.  PubMed
  1. K Arora and CL Brooks III. Functionally important conformations of the Met20 loop in dihydrofolate reductase are populated by rapid thermal fluctuations. , 2009, 131:5642–7. PMCID: PMC2889193.  PubMed
  1. DL Bostick, K Arora and CL Brooks III. K+/Na+ selectivity in toy cation binding site models is determined by the 'host'. , 2009, 96:3887–96. PMCID: PMC2712193.  PubMed
  1. DL Bostick and CL Brooks III. Statistical determinants of selective ionic complexation: ions in solvent, transport proteins, and other "hosts". , 2009, 96:4470–92. PMCID: PMC2894556.  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. , 2009, 30:1545–614. PMCID: PMC2810661.  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. , 2009, 37:D436–42. PMCID: PMC2686430.  PubMed
  1. RD Hills and CL Brooks III. Insights from coarse-grained Go models for protein folding and dynamics. , 2009, 10:889–905. PMCID: PMC2672008.  PubMed
  1. JL Knight and CL Brooks III. Lambda-dynamics free energy simulation methods. , 2009, 30:1692–700. PMCID: PMC2730455.  PubMed
  1. JL Knight and CL Brooks III. Validating CHARMM parameters and exploring charge distribution rules in structure-based drug design. , 2009, 5:1680–1691. PMCID: PMC2719862.  PubMed
  1. RV Mannige and CL Brooks III. Geometric considerations in virus capsid size specificity, auxiliary requirements, and buckling. , 2009, 106:8531–6. PMCID: PMC2688982.  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. , 2009, 8:455–63. PMCID: PMC2728591.  PubMed
  1. M Michino and CL Brooks III. Predicting structurally conserved contacts for homologous proteins using sequence conservation filters. , 2009, 77:448–53. PMCID: PMC2740814.  PubMed
  1. HD Nguyen, VS Reddy and CL Brooks III. Invariant polymorphism in virus capsid assembly. , 2009, 131:2606–14. PMCID: PMC2768263.  PubMed
  1. M Taufer, R Armen, J Chen, P Teller and CL Brooks III. Computational multiscale modeling in protein--ligand docking. , 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. , 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. , 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. , 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. , 2008, 73:644–655.  PubMed
  1. J Chen and CL Brooks III. Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions. , 2008, 10:471–81.  PubMed
  1. J Chen, CL Brooks III and J Khandogin. Recent advances in implicit solvent-based methods for biomolecular simulations. , 2008, 18:140–8. PMCID: PMC2386893.  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. , 2008, 112:242–9. PMCID: PMC2561919.  PubMed
  1. RD Hills Jr and CL Brooks III. Subdomain competition, cooperativity, and topological frustration in the folding of CheY. , 2008, 382:485–95. PMCID: PMC2564871.  PubMed
  1. RD Hills Jr and CL Brooks III. Coevolution of function and the folding landscape: correlation with density of native contacts. , 2008, 95:L57–9. PMCID: PMC2567933.  PubMed
  1. J Lee, J Chen, CL Brooks III and W Im. Application of solid-state NMR restraint potentials in membrane protein modeling. , 2008, 193:68–76. PMCID: PMC2546517.  PubMed
  1. RV Mannige and CL Brooks III. Tilable nature of virus capsids and the role of topological constraints in natural capsid design. , 2008, 77:051902. PMCID: PMC2756041.  PubMed
  1. HD Nguyen and CL Brooks III. Generalized structural polymorphism in self-assembled viral particles. , 2008, 8:4574–81. PMCID: PMC2772182.  PubMed
  1. MA Olson, M Feig and CL Brooks III. Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions. , 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. , 2008, 105:5891–6. PMCID: PMC2311355.  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. , 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. , 2007, 104:18496–501. PMCID: PMC2141805.  PubMed
  1. DL Bostick and CL Brooks III. Selectivity in K+ channels is due to topological control of the permeant ion's coordinated state. , 2007, 104:9260–5. PMCID: PMC1890482.  PubMed
  1. DL Bostick and CL Brooks III. On the equivalence point for ammonium (de)protonation during its transport through the AmtB channel. , 2007, 92:L103–5. PMCID: PMC1877791.  PubMed
  1. DL Bostick and CL Brooks III. Deprotonation by dehydration: the origin of ammonium sensing in the AmtB channel. , 2007, 3:e22. PMCID: PMC1796661.  PubMed
  1. L Bu, W Im and CL Brooks III. Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations. , 2007, 92:854–63. PMCID: PMC1779983.  PubMed
  1. J Chen and CL Brooks III. Can molecular dynamics simulations provide high-resolution refinement of protein structure. , 2007, 67:922–30.  PubMed
  1. J Chen and CL Brooks III. Critical importance of length-scale dependence in implicit modeling of hydrophobic interactions. , 2007, 129:2444–5. PMCID: PMC2551325.  PubMed
  1. RD Hills Jr and CL Brooks III. Hydrophobic cooperativity as a mechanism for amyloid nucleation. , 2007, 368:894–901. PMCID: PMC1997311.  PubMed
  1. J Khandogin and CL Brooks III. Linking folding with aggregation in Alzheimer's beta-amyloid peptides. , 2007, 104:16880–5. PMCID: PMC2040412.  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. , 2007, 129:3056–7. PMCID: PMC2546516.  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. , 2007, 16:1087–100. PMCID: PMC2206655.  PubMed
  1. HD Nguyen, VS Reddy and CL Brooks III. Deciphering the kinetic mechanism of spontaneous self-assembly of icosahedral capsids. , 2007, 7:338–44.  PubMed
  1. IF Thorpe and CL Brooks III. Molecular evolution of affinity and flexibility in the immune system. , 2007, 104:8821–6. PMCID: PMC1885586.  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

Conference Proceedings

  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. In 2007 IEEE International Parallel and Distributed Processing Symposium.

2006

Journal Article

  1. J Chen, W Im and CL Brooks III. Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field. , 2006, 128:3728–36. PMCID: PMC2596729.  PubMed
  1. J Khandogin and CL Brooks III. Toward the accurate first-principles prediction of ionization equilibria in proteins. , 2006, 45:9363–73.  PubMed
  1. J Khandogin, J Chen and CL Brooks III. Exploring atomistic details of pH-dependent peptide folding. , 2006, 103:18546–50. PMCID: PMC1693699.  PubMed
  1. IV Khavrutskii, K Arora and CL Brooks III. Harmonic Fourier beads method for studying rare events on rugged energy surfaces. , 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. , 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. , 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. , 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. , 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. , 2006, 34:D386–9. PMCID: PMC1347395.  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. , 2006, 80:10395–406.  PubMed
  1. F Tama and CL Brooks III. Symmetry, Form and Shape: Guiding Principles for Robustness in Macromolecular Machines. , 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. , 2006, 15:2190–200. PMCID: PMC2242606.  PubMed
  1. M Taufer, C An, A Kerstens and CL Brooks III. Predictor@Home: A "protein structure prediction supercomputer" based on global computing. , 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. , 2006, 45:4463–73. PMCID: PMC1780269.  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. , 2006, 103:13722–7. PMCID: PMC1564241.  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. , 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. , 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. , 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. , 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". , 2005, 127:4668–74.  PubMed
  1. O Guvench, DJ Price and CL Brooks III. Receptor rigidity and ligand mobility in trypsin-ligand complexes. , 2005, 58:407–17.  PubMed
  1. W Im and CL Brooks III. Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations. , 2005, 102:6771–6. PMCID: PMC1100747.  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. , 2005, 72:173–98.  PubMed
  1. J Khandogin and CL Brooks III. Constant pH molecular dynamics with proton tautomerism. , 2005, 89:141–57. PMCID: PMC1366513.  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. , 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. , 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. , 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. , 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. , 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. , 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. , 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. , 2005, 17:1627–1641.
  1. IF Thorpe and CL Brooks III. Conformational substates modulate hydride transfer in dihydrofolate reductase. , 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. , 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).
  1. M Taufer, PJ Teller, DP Anderson and CL Brooks III. Metrics for effective resource management in global computing environments. In First International Conference on e-Science and Grid Computing, Proceedings.

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. , 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. , 2004, 126:16038–47.  PubMed
  1. BN Dominy, H Minoux and CL Brooks III. An electrostatic basis for the stability of thermophilic 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. , 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. , 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. , 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. , 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. , 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. , 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. , 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. , 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. , 2004, 101:3432–7. PMCID: PMC373479.  PubMed
  1. MS Lee, FR Salsbury Jr and CL Brooks III. Constant-pH molecular dynamics using continuous titration coordinates. , 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. , 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. , 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. , 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. , 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. , 2004, 25:1504–14.  PubMed
  1. DJ Price and CL Brooks III. A modified TIP3P water potential for simulation with Ewald summation. , 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. , 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. , 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. , 2004, 147:315–26.  PubMed
  1. IF Thorpe and CL Brooks III. The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase. , 2004, 57:444–57.  PubMed
  1. J Trylska, R Konecny, F Tama, CL Brooks III and JA McCammon. Ribosome motions modulate electrostatic properties. , 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. , 2003, 13:143–145.
  1. BD Bursulaya, M Totrov, R Abagyan and CL Brooks III. Comparative study of several algorithms for flexible ligand docking. , 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. , 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. , 2003, 85:2900–18. PMCID: PMC1303570.  PubMed
  1. W Im, MS Lee and CL Brooks III. Generalized born model with a simple smoothing function. , 2003, 24:1691–702.  PubMed
  1. J Karanicolas and CL Brooks III. Improved Go-like Models Demonstrate the Robustness of Protein Folding Mechanisms Towards Non-native Interactions. , 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. , 2003, 53:740–7.  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?. , 2003, 100:3954–9. PMCID: PMC153029.  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. , 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. , 2003, 100:13916–21. PMCID: PMC283521.  PubMed
  1. TH Rod and CL Brooks III. How dihydrofolate reductase facilitates protonation of dihydrofolate. , 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. , 2003, 100:6980–5. PMCID: PMC165816.  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. , 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. , 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. , 2003, 100:9319–23. PMCID: PMC170916.  PubMed
  1. IF Thorpe and CL Brooks III. Barriers to hydride transfer in wild type and mutant dihydrofolate reductase from E-coli. , 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. , 2003, 24:1549–62.  PubMed

2002

Journal Article

  1. CL Brooks III. Protein and peptide folding explored with molecular simulations. , 2002, 35:447–54.  PubMed
  1. CL Brooks III. Protein folding: with a little help. , 2002, 420:33–4.  PubMed
  1. CL Brooks III. Viewing protein folding from many perspectives. , 2002, 99:1099–100. PMCID: PMC122148.  PubMed
  1. KV Damodaran, VS Reddy, JE Johnson and CL Brooks III. A general method to quantify quasi-equivalence in icosahedral viruses. , 2002, 324:723–37.  PubMed
  1. BN Dominy and CL Brooks III. Identifying native-like protein structures using physics-based potentials. , 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. , 2002, 319:541–54.  PubMed
  1. M Feig and CL Brooks III. Evaluating CASP4 predictions with physical energy functions. , 2002, 49:232–45.  PubMed
  1. A Fiser, M Feig, CL Brooks III and A Sali. Evolution and physics in comparative protein structure modeling. , 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. , 2002, 11:2351–61. PMCID: PMC2373711.  PubMed
  1. MS Lee, FR Salsbury Jr and CL Brooks III. Novel generalized Born methods. , 2002, 116:10606–10614.
  1. DJ Price and CL Brooks III. Modern protein force fields behave comparably in molecular dynamics simulations. , 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. , 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. , 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. , 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. , 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. , 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. , 2001, 75:11943–7. PMCID: PMC116089.  PubMed
  1. O Roche, R Kiyama and CL Brooks III. Ligand-protein database: linking protein-ligand complex structures to binding data. , 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. , 2001, 44:448–59.  PubMed
  1. KA Sharp and CL Brooks III. Theory and simulation: Old wine in new bottles. , 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. , 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. , 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. , 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. , 2000, 41:86–97.  PubMed
  1. JL Radkiewicz and CL Brooks III. Protein dynamics in enzymatic catalysis: Exploration of dihydrofolate reductase. , 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. , 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. , 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. , 1999, 121:9947–9951.
  1. BN Dominy and CL Brooks III. Development of a Generalized Born Model Parametrization for Proteins and Nucleic Acids. , 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. , 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. , 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. , 1999, 96:12512–7. PMCID: PMC22965.  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. , 1998, 8:222–6.  PubMed
  1. CL Brooks III, M Gruebele, JN Onuchic and PG Wolynes. Chemical physics of protein folding. , 1998, 95:11037–8. PMCID: PMC33893.  PubMed
  1. Z Guo and CL Brooks III. Rapid screening of binding affinities: Application of the l-dynamics method to a trypsin-inhibitor system. , 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. , 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. , 1998, 74:546–58. PMCID: PMC1299407.  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. , 1998, 109:2895–2903.
  1. FB Sheinerman and CL Brooks III. Calculations on folding of segment B1 of streptococcal protein G. , 1998, 278:439–56.  PubMed
  1. FB Sheinerman and CL Brooks III. Molecular picture of folding of a small alpha/beta protein. , 1998, 95:1562–7. PMCID: PMC19093.  PubMed
  1. M Vieth, JD Hirst and CL Brooks III. Do active site conformations of small ligands correspond to low free-energy solution structures. , 1998, 12:563–72.  PubMed
  1. M Vieth, JD Hirst, BN Dominy, H Daigler and CL Brooks III. Assessing search strategies for flexible docking. , 1998, 19:1623–1631.
  1. M Vieth, JD Hirst, A Kolinski and CL Brooks III. Assessing energy functions for flexible docking. , 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. , 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. , 1997, 94:10161–6. PMCID: PMC23332.  PubMed
  1. JD Hirst, DM Hirst and CL Brooks III. Multireference Configuration Interaction Calculations of Electronic States of N-Methylformamide, Acetamide, and N-Methylacetamide. , 1997, 101:4821–4827.
  1. FB Sheinerman and CL Brooks III. A molecular dynamics simulation study of segment B1 of protein G. , 1997, 29:193–202.  PubMed
  1. WA Shirley and CL Brooks III. Curious structure in "canonical" alanine-based peptides. , 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. , 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. , 1996, 100:2546–9.
  1. CL Brooks III, CB Post and P Rossky. Martin Karplus - Biography. , 1996, 100:2458–2474.
  1. JD Hirst, DM Hirst and CL Brooks III. Ab Initio Calculations of the Excited States of Formamide. , 1996, 100:13487–13491.
  1. JD Hirst, M Vieth, J Skolnick and CL Brooks III. Predicting leucine zipper structures from sequence. , 1996, 9:657–62.  PubMed
  1. XJ Kong and CL Brooks III. λ-Dynamics: A new approach to free energy calculations. , 1996, 105:2414–2423.
  1. K Oesapay, WS Young, D Bashford, CL Brooks III and DA Case. Dielectric Continuum Models for Hydration Effects on Peptide Conformational Transitions. , 1996, 100:2698–705.
  1. T Simonson and CL Brooks III. Charge Screening and the Dielectric Constant of Proteins: Insights from Molecular Dynamics. , 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. , 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. , 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. , 1996, 259:560–72.  PubMed

Book Chapter

  1. ME Karpen and CL Brooks III. Modeling protein conformation by molecular mechanics and dynamics. In Protein Structure Prediction: A Practical Approach. Edited by MJE Sternberg. Published by Oxford University Press. In Protein Structure Prediction: A Practical Approach

1995

Journal Article

  1. EM Boczko and CL Brooks III. First-principles calculation of the folding free energy of a three-helix bundle protein. , 1995, 269:393–6.  PubMed
  1. CL Brooks III. Methodological advances in molecular dynamics simulations of biological systems. , 1995, 5:211–5.  PubMed
  1. JD Hirst and CL Brooks III. Molecular dynamics simulations of isolated helices of myoglobin. , 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. , 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. , 1995, 251:448–67.  PubMed
  1. WS Young and CL Brooks III. Dynamic load balancing algorithms for replicated data molecular dynamics. , 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. , 1994, 243:173–8.  PubMed
  1. C Tsoo and C Brooks III. Cluster Structure Determination Using Gaussian Density Annealing. , 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. , 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. , 1994, 15:44–53.

1993

Journal Article

  1. EM Boczko and CL Brooks III. Constant-temperature free energy surfaces for physical and chemical processes. , 1993, 97:4509–13.
  1. C Brooks III and DA Case. Simulations of peptide conformational dynamics and thermodynamics. , 1993, 93:2487–502.
  1. CL Brooks III. Molecular simulations of peptide and protein unfolding: In quest of a molten globule. , 1993, 3:92–8.
  1. CL Brooks III and L Nilsson. Promotion of helix formation in peptides dissolved in alcohol and water-alcohol mixtures. , 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. , 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. , 1993, 3:414–23.  PubMed

Book Chapter

  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

1992

Journal Article

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

1991

Journal Article

  1. CL Brooks III, WS Young and DJ Tobias. Molecular Simulations on Supercomputers. , 1991, 5:98–112.
  1. T Head-Gordon and CL Brooks III. Virtual rigid body dynamics. , 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. , 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. , 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. , 1991, 113:2295–301.
  1. DR McKelvey, CL Brooks and M Mokotoff. A CHARMM analysis of the conformations of the metastasis-inhibiting laminin pentapeptide. , 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. , 1991, 12:1270–7.
  1. DJ Tobias and CL Brooks III. Thermodynamics and mechanism of alpha helix initiation in alanine and valine peptides. , 1991, 30:6059–70.  PubMed
  1. DJ Tobias, JE Mertz and CL Brooks III. Nanosecond time scale folding dynamics of a pentapeptide in water. , 1991, 30:6054–8.  PubMed
  1. DJ Tobias, SF Sneddon and CL Brooks III. The stability of protein secondary structures in aqueous solution. , 1991, 239:174–99.

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

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. , 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. , 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. , 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. , 1990, 92:2582–92.
  1. DJ Tobias, SF Sneddon and CL Brooks III. Reverse turns in blocked dipeptides are intrinsically unstable in water. , 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. , 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. , 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. , 1989, 16:311–22.
  1. SF Sneddon, RS Morgan and CL Brooks III. Toward a model of electronic coupling in proteins. , 1989, 93:8115–18.
  1. SF Sneddon, DJ Tobias and CL Brooks III. Thermodynamics of amide hydrogen bond formation in polar and apolar solvents. , 1989, 209:817–20.  PubMed
  1. DJ Tobias, CL Brooks III and SH Fleischman. Conformational flexibility in free energy simulations. , 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. , 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. , 1988, 53:83–9. PMCID: 1330124.  PubMed
  1. DJ Tobias and CL Brooks III. Molecular dynamics with internal coordinate constraints. , 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

Book Chapter

  1. CL Brooks III. Thermodynamic calculations on biological molecules. In Computer Simulations of Biomolecular Systems: Theoretical and Experimental Applications. Edited by W van Gunsteren, P Weiner. Published by International Journal of Quantum Chemistry, Quantum Biology Symposium (Princeton, N.J.). Volume: 15, In Computer Simulations of Biomolecular Systems: Theoretical and Experimental Applications

1987

Journal Article

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

1986

Journal Article

  1. CL Brooks III. Thermodynamics of ionic solvation: Monte Carlo simulations of aqueous chloride and bromide ions. , 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. , 1986, 471:295–8.

Book Chapter

  1. CL Brooks III and M Karplus. Theoretical approaches to solvation of biopolymers. In Methods in Enzymology. Published by Academic Press. Volume: 127, In 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. , 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. , 1985, 83:5897–908.
  1. AT Brunger, CL Brooks III and M Karplus. Active site dynamics of ribonuclease. , 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. , 1984, 80:5598–609.
  1. A Bruenger, CL Brooks III and M Karplus. Stochastic boundary conditions for molecular dynamics simulations of ST2 water. , 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. , 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. , 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. , 1983, 79:784–803.
  1. CL Brooks III and M Karplus. Deformable stochastic boundaries in molecular dynamics. , 1983, 79:6312–25.

1982

Journal Article

  1. SA Adelman and CL Brooks III. Generalized Langevin models and condensed-phase chemical reaction dynamics. , 1982, 86:1511–24.
  1. CL Brooks III and SA Adelman. Dynamics of liquid state chemical reactions: modeling of R-dependent correlation functions. , 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. , 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. , 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. , 1980, 73:4353–64.

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