Laboratory of Computational Biophysics

Publications

2022

"Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches," P. S. Hudson, F. Aviat, R. Meana-Pañeda, L. Warrensford, B. C. Pollard, S. Prasad, M. R. Jones, H. L. Woodcock and B. R. Brooks, Journal of Computer-Aided Molecular Design, 36 (4) pp. 263-277 (2022). [DOI] [URL]

"GraphVAMPNet, using graph neural networks and variational approach to Markov processes for dynamical modeling of biomolecules," M. Ghorbani, S. Prasad, J. B. Klauda and B. R. Brooks, The Journal of Chemical Physics, 156 (18) pp. 184103 (2022). [DOI] [URL]

"Protein pK_a Prediction by Tree-Based Machine Learning," A. Y. Chen, J. Lee, A. Damjanovic and B. R. Brooks, Journal of Chemical Theory and Computation, 18 (4) pp. 2673-2686 (2022). [DOI] [URL]

"CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems," Y. K. Choi, N. R. Kern, S. Kim, K. Kanhaiya, Y. Afshar, S. H. Jeon, S. Jo, B. R. Brooks, J. Lee, E. B. Tadmor, H. Heinz and W. Im, Journal of Chemical Theory and Computation, 18 (1) pp. 479-493 (2022). [DOI] [URL]

2021

"Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package," E. Epifanovsky, A. T. B. Gilbert, X. Feng, J. Lee, Y. Mao, N. Mardirossian, P. Pokhilko, A. F. White, M. P. Coons, A. L. Dempwolff, Z. Gan, D. Hait, P. R. Horn, L. D. Jacobson, I. Kaliman, J. Kussmann, A. W. Lange, K. U. Lao, D. S. Levine, J. Liu, S. C. McKenzie, A. F. Morrison, K. D. Nanda, F. Plasser, D. R. Rehn, M. L. Vidal, Z.-Q. You, Y. Zhu, B. Alam, B. J. Albrecht, A. Aldossary, E. Alguire, J. H. Andersen, V. Athavale, D. Barton, K. Begam, A. Behn, N. Bellonzi, Y. A. Bernard, E. J. Berquist, H. G. A. Burton, A. Carreras, K. Carter-Fenk, R. Chakraborty, A. D. Chien, K. D. Closser, V. Cofer-Shabica, S. Dasgupta, M. de Wergifosse, J. Deng, M. Diedenhofen, H. Do, S. Ehlert, P.-T. Fang, S. Fatehi, Q. Feng, T. Friedhoff, J. Gayvert, Q. Ge, G. Gidofalvi, M. Goldey, J. Gomes, C. E. González-Espinoza, S. Gulania, A. O. Gunina, M. W. D. Hanson-Heine, P. H. P. Harbach, A. Hauser, M. F. Herbst, M. Hernández Vera, M. Hodecker, Z. C. Holden, S. Houck, X. Huang, K. Hui, B. C. Huynh, M. Ivanov, Á. Jász, H. Ji, H. Jiang, B. Kaduk, S. Kähler, K. Khistyaev, J. Kim, G. Kis, P. Klunzinger, Z. Koczor-Benda, J. H. Koh, D. Kosenkov, L. Koulias, T. Kowalczyk, C. M. Krauter, K. Kue, A. Kunitsa, T. Kus, I. Ladjánszki, A. Landau, K. V. Lawler, D. Lefrancois, S. Lehtola, R. R. Li, Y.-P. Li, J. Liang, M. Liebenthal, H.-H. Lin, Y.-S. Lin, F. Liu, K.-Y. Liu, M. Loipersberger, A. Luenser, A. Manjanath, P. Manohar, E. Mansoor, S. F. Manzer, S.-P. Mao, A. V. Marenich, T. Markovich, S. Mason, S. A. Maurer, P. F. McLaughlin, M. F. S. J. Menger, J.-M. Mewes, S. A. Mewes, P. Morgante, J. W. Mullinax, K. J. Oosterbaan, G. Paran, A. C. Paul, S. K. Paul, F. Pavošević, Z. Pei, S. Prager, E. I. Proynov, Á. Rák, E. Ramos-Cordoba, B. Rana, A. E. Rask, A. Rettig, R. M. Richard, F. Rob, E. Rossomme, T. Scheele, M. Scheurer, M. Schneider, N. Sergueev, S. M. Sharada, W. Skomorowski, D. W. Small, C. J. Stein, Y.-C. Su, E. J. Sundstrom, Z. Tao, J. Thirman, G. J. Tornai, T. Tsuchimochi, N. M. Tubman, S. P. Veccham, O. Vydrov, J. Wenzel, J. Witte, A. Yamada, K. Yao, S. Yeganeh, S. R. Yost, A. Zech, I. Y. Zhang, X. Zhang, Y. Zhang, D. Zuev, A. Aspuru-Guzik, A. T. Bell, N. A. Besley, K. B. Bravaya, B. R. Brooks, D. Casanova, J.-D. Chai, S. Coriani, C. J. Cramer, G. Cserey, A. E. DePrince, R. A. DiStasio, A. Dreuw, B. D. Dunietz, T. R. Furlani, W. A. Goddard, S. Hammes-Schiffer, T. Head-Gordon, W. J. Hehre, C.-P. Hsu, T.-C. Jagau, Y. Jung, A. Klamt, J. Kong, D. S. Lambrecht, W. Liang, N. J. Mayhall, C. W. McCurdy, J. B. Neaton, C. Ochsenfeld, J. A. Parkhill, R. Peverati, V. A. Rassolov, Y. Shao, L. V. Slipchenko, T. Stauch, R. P. Steele, J. E. Subotnik, A. J. W. Thom, A. Tkatchenko, D. G. Truhlar, T. Van Voorhis, T. A. Wesolowski, K. B. Whaley, H. L. Woodcock, P. M. Zimmerman, S. Faraji, P. M. W. Gill, M. Head-Gordon, J. M. Herbert and A. I. Krylov, The Journal of Chemical Physics, 155 (8) pp. 084801 (2021). [DOI] [URL]

"Determinants of conductance of a bacterial voltage-gated sodium channel," A. Y. Chen, B. R. Brooks and A. Damjanovic, Biophysical Journal, 120 (15) pp. 3050-3069 (2021). [DOI] [URL]

"Replica Exchange Molecular Dynamics of Diphenylalanine Amyloid Peptides in Electric Fields," B. Narayan, C. Herbert, B. J. Rodriguez, B. R. Brooks and N.-V. Buchete, The Journal of Physical Chemistry B, 125 (20) pp. 5233-5242 (2021). [DOI] [URL]

"Analytical Hessians for Ewald and particle mesh Ewald electrostatics," A. C. Simmonett and B. R. Brooks, The Journal of Chemical Physics, 154 (10) pp. 104101 (2021). [DOI] [URL]

"Exploring dynamics and network analysis of spike glycoprotein of SARS-COV-2," M. Ghorbani, B. R. Brooks and J. B. Klauda, Biophysical Journal, 120 (14) pp. 2902-2913 (2021). [DOI] [URL]

"Variational embedding of protein folding simulations using Gaussian mixture variational autoencoders," M. Ghorbani, S. Prasad, J. B. Klauda and B. R. Brooks, The Journal of Chemical Physics, 155 (19) pp. 194108 (2021). [DOI] [URL]

"The Extended Eighth-Shell method for periodic boundary conditions with rotational symmetry," S. Prasad, A. C. Simmonett, R. Meana-Pañeda and B. R. Brooks, Journal of Computational Chemistry, 42 (19) pp. 1373-1383 (2021). [DOI] [URL]

"A replica exchange umbrella sampling (REUS) approach to predict host-guest binding free energies in SAMPL8 challenge," G. Mahdi, P. S. Hudson, F. Aviat, R. Meana-Pañeda, M. R. Jones, J. B. Klauda and B. R. Brooks, Journal of Computer-Aided Molecular Design, 35 (5) pp. 667-677 (2021). [DOI]

"Improving the speed of volumetric density map generation via cubic spline interpolation," D. R. Roe and B. R. Brooks, Journal of Molecular Graphics and Modelling, 104 pp. 107832 (2021). [DOI] [URL]

"Determination of van der Waals Parameters Using a Double Exponential Potential for Nonbonded Divalent Metal Cations in TIP3P Solvent," V. H. Man, X. Wu, X. He, X.-Q. Xie, B. R. Brooks and J. Wang, Journal of Chemical Theory and Computation, (in press) (2021). [DOI] [URL]

"CHARMM36 Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for PE, PG, and Ether Lipids," Y. Yu, A. Krämer, R. Venable, B. Brooks, J. Klauda and R. Pastor, Journal of Chemical Theory and Computation, (in press) (2021). [DOI]

"Semi-Automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion," Y. Yu, A. Krämer, A. Simmonett, R. Venable, A. MacKerell, J. Klauda, R. W. Pastor and B. Brooks, Journal of Chemical Theory and Computation, (in press) (2021). [DOI] [URL]

"Molecular Simulation Study on the Walking Mechanism of Kinesin Dimers on Microtubules," A. Pan, A. Pan, B. R. Brooks and X. Wu, Current Advances in Chemistry and Biochemistry Vol. 1, pp. 49-64 (2021). [DOI] [URL]

"Correlation Between Water Molecules Identified in Atomic Models of Beta-Galactosidase Determined by Cryo-EM and X-Ray Crystallography," F. Tofoleanu, L. Earl, F. Pickard and B. Brooks, (2021). [DOI] [URL]

"A compression strategy for particle mesh Ewald theory," A. C. Simmonett and B. R. Brooks, The Journal of Chemical Physics, 154 (5) pp. 054112 (2021). [DOI] [URL]

2020

"Membrane permeability of small molecules from unbiased molecular dynamics simulations," A. Krämer, A. Ghysels, E. Wang, R. M. Venable, J. B. Klauda, B. R. Brooks and R. W. Pastor, The Journal of Chemical Physics, 153 (12) pp. 124107 (2020). [DOI] [URL]

"Hierarchical Markov State Model Building to Describe Molecular Processes," D. K. Wolfe, J. R. Persichetti, A. K. Sharma, P. S. Hudson, H. L. Woodcock and E. P. O'Brien, Journal of Chemical Theory and Computation, 16 (3) pp. 1816-1826 (2020). [DOI] [URL]

"Critical Sequence Hotspots for Binding of Novel Coronavirus to Angiotensin Converter Enzyme as Evaluated by Molecular Simulations," M. Ghorbani, B. R. Brooks and J. B. Klauda, The Journal of Physical Chemistry B, 124 (45) pp. 10034-10047 (2020). [DOI] [URL]

"Enantiomerization of Axially Chiral Biphenyls: Polarizable MD Simulations in Water and Butylmethylether," V. Zeindlhofer, P. Hudson, Á. M. Pálvölgyi, M. Welsch, M. Almarashi, H. L. Woodcock, B. Brooks, K. Bica-Schröder and C. Schröder, International journal of molecular sciences, 21 (17) pp. 6222 (2020). [DOI] [URL]

"Reformulation of the self-guided molecular simulation method," X. Wu and B. R. Brooks, The Journal of Chemical Physics, 153 (9) pp. 094112 (2020). [DOI] [URL]

"Membrane cholesterol dependence of cannabinoid modulation of glycine receptor," L. Yao, M. Wells, X. Wu, Y. Xu, L. Zhang and W. Xiong, The FASEB Journal, 34 (8) pp. 10920-10930 (2020). [DOI] [URL]

"A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations," D. R. Roe and B. R. Brooks, The Journal of Chemical Physics, 153 (5) pp. 054123 (2020). [DOI] [URL]

"PSI4 1.4: Open-source software for high-throughput quantum chemistry," D. G. A. Smith, L. A. Burns, A. C. Simmonett, R. M. Parrish, M. C. Schieber, R. Galvelis, P. Kraus, H. Kruse, R. Di Remigio, A. Alenaizan, A. M. James, S. Lehtola, J. P. Misiewicz, M. Scheurer, R. A. Shaw, J. B. Schriber, Y. Xie, Z. L. Glick, D. A. Sirianni, J. S. O'Brien, J. M. Waldrop, A. Kumar, E. G. Hohenstein, B. P. Pritchard, B. R. Brooks, H. F. Schaefer, A. Y. Sokolov, K. Patkowski, A. E. DePrince, U. Bozkaya, R. A. King, F. A. Evangelista, J. M. Turney, T. D. Crawford and C. D. Sherrill, The Journal of Chemical Physics, 152 (18) pp. 184108 (2020). [DOI] [URL]

"Direct global optimization of Onsager-Machlup action using Action-CSA" J. L. and B. R. Brooks", Chemical Physics, 535 pp. 110768 (2020). [DOI] [URL]

"Protonation state of the selectivity filter of bacterial voltage-gated sodium channels is modulated by ions," A. Damjanovic, A. Y. Chen, R. L. Rosenberg, D. R. Roe, X. Wu and B. R. Brooks, Proteins: Structure, Function, and Bioinformatics, 88 (3) pp. 527-539 (2020). [DOI] [URL]

"Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water–octanol partition coefficients in the SAMPL6 challenge," A. Krämer, P. S. Hudson, M. R. Jones and B. R. Brooks, Journal of Computer-Aided Molecular Design, 34 (5) pp. 471-483 (2020). [DOI] [URL]

"Quantum chemical predictions of water–octanol partition coefficients applied to the SAMPL6 logP blind challenge," M. R. Jones and B. R. Brooks, Journal of Computer-Aided Molecular Design, 34 (5) pp. 485-493 (2020). [DOI] [URL]

"SAMPL6 logP challenge: machine learning and quantum mechanical approaches," P. Patel, D. M. Kuntz, M. R. Jones, B. R. Brooks and A. K. Wilson, Journal of Computer-Aided Molecular Design, 34 (5) pp. 495-510 (2020). [DOI] [URL]

"A deep learning approach for the blind logP prediction in SAMPL6 challenge," S. Prasad and B. R. Brooks, Journal of Computer-Aided Molecular Design, 34 (5) pp. 535-542 (2020). [DOI] [URL]

2019

"Albumin-chaperoned cyanine dye yields superbright NIR-II fluorophore with enhanced pharmacokinetics," R. Tian, Q. Zeng, S. Zhu, J. Lau, S. Chandra, R. Ertsey, K. S. Hettie, T. Teraphongphom, Z. Hu, G. Niu, D. O. Kiesewetter, H. Sun, X. Zhang, A. L. Antaris, B. R. Brooks and X. Chen, Science Advances, 5 (9) (2019). [DOI] [URL]

"An Albumin Sandwich Enhances in Vivo Circulation and Stability of Metabolically Labile Peptides," R. Tian, S. Zhu, Q. Zeng, L. Lang, Y. Ma, D. O. Kiesewetter, Y. Liu, X. Fu, J. Lau, G. Zhu, O. Jacobson, Z. Wang, Y. Dai, G. Yu, B. R. Brooks, G. Liu, G. Niu and X. Chen, Bioconjugate Chemistry, 30 (6) pp. 1711-1723 (2019). [DOI] [URL]

"Use of Interaction Energies in QM/MM Free Energy Simulations," P. S. Hudson, H. L. Woodcock and S. Boresch, Journal of Chemical Theory and Computation, 15 (8) pp. 4632-4645 (2019). [DOI] [URL]

"Interactions of Water and Alkanes: Modifying Additive Force Fields to Account for Polarization Effects," A. Krämer, F. C. Pickard, J. Huang, R. M. Venable, A. C. Simmonett, D. Reith, K. N. Kirschner, R. W. Pastor and B. R. Brooks, Journal of Chemical Theory and Computation, 15 (6) pp. 3854-3867 (2019). [DOI] [URL]

"The homogeneity condition: A simple way to derive isotropic periodic sum potentials for efficient calculation of long-range interactions in molecular simulation," X. Wu and B. R. Brooks, The Journal of Chemical Physics, 150 (21) pp. 214109 (2019). [DOI] [URL]

"A double exponential potential for van der Waals interaction," X. Wu and B. R. Brooks, AIP Advances, 9 (6) pp. 065304 (2019). [DOI] [URL]

"Protein-Protein Docking Using Map Objects," X. Wu and B. R. Brooks, , In Molecular Docking and Molecular Dynamics. IntechOpen. (2019). [DOI]

2018

"Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching," P. S. Hudson, S. Boresch, D. M. Rogers and H. L. Woodcock, Journal of Chemical Theory and Computation, 14 (12) pp. 6327-6335 (2018). [DOI] [URL]

"Origins of the Mechanochemical Coupling of Peptide Bond Formation to Protein Synthesis," B. Fritch, A. Kosolapov, P. Hudson, D. A. Nissley, H. L. Woodcock, C. Deutsch and E. P. O'Brien, Journal of the American Chemical Society, 140 (15) pp. 5077-5087 (2018). [DOI] [URL]

"Deriving the Open State Structure of Glutamate Receptor through MapSGLD Flexible Fitting into Cryo-Electron Microscopy Maps," X. Wu and B. R. Brooks, , In Proceedings of the World Congress on Engineering and Computer Science. 1 (2018). [URL]

"Amyloid Fibril Design: Limiting Structural Polymorphism in Alzheimer's Aβ Protofilaments," B. Tywoniuk, Y. Yuan, S. McCartan, B. M. Szydłowska, F. Tofoleanu, B. R. Brooks and N.-V. Buchete, The Journal of Physical Chemistry B, 122 (49) pp. 11535-11545 (2018). [DOI] [URL]

"Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale," P. S. Hudson, K. Han, H. L. Woodcock and B. R. Brooks, Journal of Computer-Aided Molecular Design, 32 (10) pp. 983-999 (2018). [DOI] [URL]

"Impact of intracellular ionic strength on dimer binding in the NF-kB Inducing kinase," M. R. Jones, J. Yue and A. K. Wilson, Journal of Structural Biology, 202 (3) pp. 183 - 190 (2018). [DOI] [URL]

"A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes," G. König, F. C. Pickard, J. Huang, W. Thiel, A. D. MacKerell, B. R. Brooks and D. M. York, Molecules, 23 (10) (2018). [DOI] [URL]

"Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host–guest challenges," N. Nishikawa, K. Han, X. Wu, F. Tofoleanu and B. R. Brooks, Journal of Computer-Aided Molecular Design, 32 (10) pp. 1075-1086 (2018). [DOI] [URL]

"An explicit-solvent hybrid QM and MM approach for predicting pK_a of small molecules in SAMPL6 challenge," S. Prasad, J. Huang, Q. Zeng and B. R. Brooks, Journal of Computer-Aided Molecular Design, 32 (10) pp. 1191-1201 (2018). [DOI] [URL]

"Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations," F. Tofoleanu, Y. Yuan, F. C. Pickard, B. Tywoniuk, B. R. Brooks and N.-V. Buchete, The Journal of Physical Chemistry B, 122 (21) pp. 5657-5665 (2018). [DOI] [URL]

"Hydronium Ions Accompanying Buried Acidic Residues Lead to High Apparent Dielectric Constants in the Interior of Proteins," X. Wu and B. R. Brooks, The Journal of Physical Chemistry B, 122 (23) pp. 6215-6223 (2018). [DOI] [URL]

"Reservoir pH replica exchange," A. Damjanovic, B. T. Miller, A. Okur and B. R. Brooks, The Journal of Chemical Physics, 149 (7) pp. 072321 (2018). [DOI] [URL]

"Conformational analysis of replica exchange MD: Temperature-dependent Markov networks for FF amyloid peptides," B. Narayan, C. Herbert, Y. Yuan, B. J. Rodriguez, B. R. Brooks and N.-V. Buchete, The Journal of Chemical Physics, 149 (7) pp. 072323 (2018). [DOI] [URL]

"On the convergence of multi-scale free energy simulations," G. König, B. R. Brooks, W. Thiel and D. M. York, Molecular Simulation, 44 (13-14) pp. 1062-1081 (2018). [DOI] [URL]

"SAMPL6 host--guest challenge: binding free energies via a multistep approach," Y. Eken, P. Patel, T. Díaz, M. R. Jones and A. K. Wilson, Journal of Computer-Aided Molecular Design, 32 (10) pp. 1097-1115 (2018). [DOI] [URL]

"Prediction of CB[8] host–guest binding free energies in SAMPL6 using the double-decoupling method," K. Han, P. S. Hudson, M. R. Jones, N. Nishikawa, F. Tofoleanu and B. R. Brooks, Journal of Computer-Aided Molecular Design, 32 (10) pp. 1059-1073 (2018). [DOI] [URL]

"Absolute and relative pK_a predictions via a DFT approach applied to the SAMPL6 blind challenge," Q. Zeng, M. R. Jones and B. R. Brooks, Journal of Computer-Aided Molecular Design, 32 (10) pp. 1179-1189 (2018). [DOI] [URL]

"Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions Using Alkane Simulations," A. N. Leonard, A. C. Simmonett, F. C. Pickard, J. Huang, R. M. Venable, J. B. Klauda, B. R. Brooks and R. W. Pastor, Journal of Chemical Theory and Computation, 14 (2) pp. 948-958 (2018). [DOI] [URL]

2017

"Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level," M. Wang, P. Li, X. Jia, W. Liu, Y. Shao, W. Hu, J. Zheng, B. R. Brooks and Y. Mei, Journal of Chemical Information and Modeling, 57 (10) pp. 2476-2489 (2017). [DOI] [URL]

"Global organization of a binding site network gives insight into evolution and structure-function relationships of proteins," J. Lee, J. Konc, D. Janezic and B. R. Brooks, Scientific Reports, 7 (1) pp. 11652 (2017). [DOI] [URL]

"Inverse Resolution Limit of Partition Density and Detecting Overlapping Communities by Link-Surprise," J. Lee, Z.-Y. Zhang, J. Lee, B. R. Brooks and Y.-Y. Ahn, Scientific Reports, 7 (1) pp. 12399 (2017). [DOI] [URL]

"An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches," J. Huang, Y. Mei, G. König, A. C. Simmonett, F. C. Pickard IV, Q. Wu, L.-P. Wang, A. D. MacKerell, B. R. Brooks and Y. Shao, Journal of Chemical Theory and Computation, 13 (2) pp. 679-695 (2017). [DOI] [URL]

"OpenMM 7: Rapid development of high performance algorithms for molecular dynamics," P. Eastman, J. Swails, J. D. Chodera, R. T. McGibbon, Y. Zhao, K. A. Beauchamp, L.-P. Wang, A. C. Simmonett, M. P. Harrigan, C. D. Stern, R. P. Wiewiora, B. R. Brooks and V. S. Pande, PLoS Computational Biology, 13 (7) pp. e1005659 (2017). [DOI] [URL]

"Mapping the Drude polarizable force field onto a multipole and induced dipole model," J. Huang, A. C. Simmonett, F. C. Pickard IV, A. D. MacKerell Jr and B. R. Brooks, The Journal of Chemical Physics, 147 (16) pp. 161702 (2017). [DOI] [URL]

"Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge," J. Lee, F. Tofoleanu, F. C. Pickard IV, G. König, J. Huang, A. Damjanović, M. Baek, C. Seok and B. R. Brooks, Journal of Computer-Aided Molecular Design, 31 (1) pp. 71-85 (2017). [DOI] [URL]

"Finding multiple reaction pathways via global optimization of action," J. Lee, I.-H. Lee, I. Joung, J. Lee and B. R. Brooks, Nature Communications, 8 (2017). [DOI] [URL]

"Machine Learning Force Field Parameters from Ab Initio Data," Y. Li, H. Li, F. C. Pickard IV, B. Narayanan, F. Sen, M. K. Chan, S. Sankaranarayanan, B. R. Brooks and B. Roux, Journal of Chemical Theory and Computation, 13 (9) pp. 4492-4503 (2017). [DOI] [URL]

"Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability," R. M. Parrish, L. A. Burns, D. G. Smith, A. C. Simmonett, A. E. DePrince, E. G. Hohenstein, U. Bozkaya, A. Y. Sokolov, R. Di Remigio, R. M. Richard, J. F. Gonthier, James Andrew M, MacAlexander Harley R, Kumar Ashutosh, Salton Masaaki, Wang Xiao, Pritchard Benjamin P, Verma Prakash, Schaefer III Henry F, Patkowski Konrad, King Rollin A, Valeev Edward F, Evangelista Francesco A, Turney Justin M, Carawford T Daniel and C. D. Sherrill, Journal of Chemical Theory and Computation, 13 (7) pp. 3185-3197 (2017). [DOI] [URL]

"Absolute binding free energies for octa-acids and guests in SAMPL5," F. Tofoleanu, J. Lee, F. C. Pickard IV, G. König, J. Huang, M. Baek, C. Seok and B. R. Brooks, Journal of Computer-Aided Molecular Design, 31 (1) pp. 107-118 (2017). [DOI] [URL]

2016

"Structure and Dynamics of Macromolecular Assemblies from Electron Microscopy Maps," X. Wu and B. R. Brooks, , In Modern Electron Microscopy in Physical and Life Sciences. pp. 243-262 INTECH Open Access Publisher. (2016). [DOI] [URL]

"Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method," G. König, Y. Mei, F. C. Pickard IV, A. C. Simmonett, B. T. Miller, J. M. Herbert, H. L. Woodcock, B. R. Brooks and Y. Shao, Journal of Chemical Theory and Computation, 12 (1) pp. 332-344 (2016). [DOI] [URL]

"Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics," X. Jia, M. Wang, Y. Shao, G. König, B. R. Brooks, J. Z. H. Zhang and Y. Mei, Journal of Chemical Theory and Computation, 12 (2) pp. 499-511 (2016). [DOI] [URL]

"Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials," E. C. Dybeck, G. König, B. R. Brooks and M. R. Shirts, Journal of Chemical Theory and Computation, 12 (4) pp. 1466-1480 (2016). [DOI] [URL]

"Molecular Multipole Potential Energy Functions for Water," M.-L. Tan, K. N. Tran, F. C. Pickard IV, A. C. Simmonett, B. R. Brooks and T. Ichiye, The Journal of Physical Chemistry B, 120 (8) pp. 1833-1842 (2016). [DOI] [URL]

"Origin of pK_a Shifts of Internal Lysine Residues in SNase Studied Via Equal-Molar VMMS Simulations in Explicit Water," X. Wu, J. Lee and B. R. Brooks, The Journal of Physical Chemistry B, 121 (15) pp. 3310-3330 (2016). [DOI] [URL]

"Structural Characterization of Arginine Fingers: Identification of an Arginine Finger for the Pyrophosphatase dUTPases," G. N. Nagy, R. Suardíaz, A. Lopata, O. Ozohanics, K. Vékey, B. R. Brooks, I. Leveles, J. Tóth, B. G. Vértessy and E. Rosta, Journal of the American Chemical Society, 138 (45) pp. 15035-15045 (2016). [DOI] [URL]

"An empirical extrapolation scheme for efficient treatment of induced dipoles," A. C. Simmonett, F. C. Pickard IV, J. W. Ponder and B. R. Brooks, The Journal of Chemical Physics, 145 (16) pp. 164101-8 (2016). [DOI] [URL]

"Isotropic periodic sum for multipole interactions and a vector relation for calculation of the Cartesian multipole tensor," X. Wu, F. C. Pickard IV and B. R. Brooks, The Journal of Chemical Physics, 145 (16) pp. 164110 (2016). [DOI] [URL]

"The ubiquitin ligase Ubr4 controls stability of podocin/MEC-2 supercomplexes," M. M. Rinschen, P. Bharill, X. Wu, P. Kohli, M. J. Reinert, O. Kretz, I. Saez, B. Schermer, M. Höhne, M. P. Bartram, S. Aravamudhan, B. R. Brooks, D. Vilchez, T. B. Huber, R.-U. Müller, M. Krüger and T. Benzing, Human Molecular Genetics, 25 (7) pp. 1328 (2016). [DOI] [URL]

"Self-guided Langevin dynamics via generalized Langevin equation," X. Wu, B. R. Brooks and E. Vanden-Eijnden, Journal of Computational Chemistry, 37 (6) pp. 595-601 (2016). [DOI] [URL]

"Partition coefficients for the SAMPL5 challenge using transfer free energies," M. R. Jones, B. R. Brooks and A. K. Wilson, Journal of Computer-Aided Molecular Design, 30 (11) pp. 1129-1138 (2016). [DOI] [URL]

"Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge," G. König, F. C. Pickard IV, J. Huang, A. C. Simmonett, F. Tofoleanu, J. Lee, P. O. Dral, S. Prasad, M. Jones, Y. Shao, W. Thiel and B. R. Brooks, Journal of Computer-Aided Molecular Design, 30 (11) pp. 989-1006 (2016). [DOI] [URL]

"Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK_a corrections," F. C. Pickard IV, G. König, F. Tofoleanu, J. Lee, A. C. Simmonett, Y. Shao, J. W. Ponder and B. R. Brooks, Journal of Computer-Aided Molecular Design, 30 (11) pp. 1087-1100 (2016). [DOI] [URL]

"An efficient protocol for obtaining accurate hydration free energies using quantum chemistry and reweighting from molecular dynamics simulations," F. C. Pickard IV, G. König, A. C. Simmonett, Y. Shao and B. R. Brooks, Bioorganic & Medicinal Chemistry , 24 (20) pp. 4988 - 4997 (2016). [DOI] [URL]

"Computational scheme for pH-dependent binding free energy calculation with explicit solvent," J. Lee, B. T. Miller and B. R. Brooks, Protein Science, 25 (1) pp. 231-243 (2016). [DOI] [URL]

2015

"A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water," X. Wu and B. R. Brooks, PLOS Computational Biology, 11 (10) pp. 1-29 (2015). [DOI] [URL]

"2.2 Å resolution cryo-EM structure of β-galactosidase in complex with a cell-permeant inhibitor," A. Bartesaghi, A. Merk, S. Banerjee, D. Matthies, X. Wu, J. L. S. Milne and S. Subramaniam, Science, 348 (6239) pp. 1147-1151 (2015). [DOI] [URL]

"Structure and dynamics of the fibronectin-III domains of Aplysia californica cell adhesion molecules," C. M. Kelly, J. Muzard, B. R. Brooks, G. U. Lee and N.-V. Buchete, Phys. Chem. Chem. Phys., 17 pp. 9634-9643 (2015). [DOI] [URL]

"Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory," Z. Cournia, T. W. Allen, I. Andricioaei, B. Antonny, D. Baum, G. Brannigan, N.-V. Buchete, J. T. Deckman, L. Delemotte, C. del Val, R. Friedman, P. Gkeka, H.-C. Hege, J. Hénin, M. A. Kasimova, A. Kolocouris, M. L. Klein, S. Khalid, M. J. Lemieux, N. Lindow, M. Roy, J. Selent, M. Tarek, F. Tofoleanu, S. Vanni, S. Urban, D. J. Wales, J. C. Smith and A.-N. Bondar, The Journal of Membrane Biology, 248 (4) pp. 611-640 (2015). [DOI] [URL]

"ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites," J. Konc, B. T. Miller, T. Štular, S. Lešnik, H. L. Woodcock, B. R. Brooks and D. Janežiž, Journal of Chemical Information and Modeling, 55 (11) pp. 2308-2314 (2015). [DOI] [URL]

"The Atomistic Mechanism of Conformational Transition of Adenylate Kinase Investigated by Lorentzian Structure-Based Potential," J. Lee, K. Joo, B. R. Brooks and J. Lee, Journal of Chemical Theory and Computation, 11 (7) pp. 3211-3224 (2015). [DOI] [URL]

"Numerical Study on the Partitioning of the Molecular Polarizability into Fluctuating Charge and Induced Atomic Dipole Contributions," Y. Mei, A. C. Simmonett, F. C. Pickard IV, R. A. DiStasio, B. R. Brooks and Y. Shao, The Journal of Physical Chemistry A, 119 (22) pp. 5865-5882 (2015). [DOI] [URL]

"Modulation of Alzheimer's Aβ Protofilament-Membrane Interactions by Lipid Headgroups," F. Tofoleanu, B. R. Brooks and N.-V. Buchete, ACS Chemical Neuroscience, 6 (3) pp. 446-455 (2015). [DOI] [URL]

"Mutations Decouple Proton Transfer from Phosphate Cleavage in the dUTPase Catalytic Reaction," A. Lopata, P. G. Jambrina, P. K. Sharma, B. R. Brooks, J. Toth, B. G. Vertessy and E. Rosta, ACS Catalysis, 5 (6) pp. 3225-3237 (2015). [DOI] [URL]

"Enhancing Constant-pH Simulation in Explicit Solvent with a Two-Dimensional Replica Exchange Method," J. Lee, B. T. Miller, A. Damjanović and B. R. Brooks, Journal of Chemical Theory and Computation, 11 (6) pp. 2560-2574 (2015). [DOI] [URL]

"Multiple Environment Single System Quantum Mechanical/Molecular Mechanical (MESS-QM/MM) Calculations. 1. Estimation of Polarization Energies," A. J. Sodt, Y. Mei, G. König, P. Tao, R. P. Steele, B. R. Brooks and Y. Shao, The Journal of Physical Chemistry A, 119 (9) pp. 1511-1523 (2015). [DOI] [URL]

"Hydrophobic hydration and the anomalous partial molar volumes in ethanol-water mixtures," M.-L. Tan, B. T. Miller, J. Te, J. R. Cendagorta, B. R. Brooks and T. Ichiye, The Journal of Chemical Physics, 142 (6) pp. 064501 (2015). [DOI] [URL]

"Efficient treatment of induced dipoles," A. C. Simmonett, F. C. Pickard IV, Y. Shao, T. E. Cheatham III and B. R. Brooks, The Journal of Chemical Physics, 143 (7) pp. 074115 (2015). [DOI] [URL]

"Advances in molecular quantum chemistry contained in the Q-Chem 4 program package," Y. Shao, Z. Gan, E. Epifanovsky, A. T. Gilbert, M. Wormit, J. Kussmann, A. W. Lange, A. Behn, J. Deng, X. Feng, D. Ghosh, M. Goldey, P. R. Horn, L. D. Jacobson, I. Kaliman, R. Z. Khaliullin, T. Kuś, A. Landau, J. Liu, E. I. Proynov, Y. M. Rhee, R. M. Richard, M. A. Rohrdanz, R. P. Steele, E. J. Sundstrom, III H. Lee Woodcock, P. M. Zimmerman, D. Zuev, B. Albrecht, E. Alguire, B. Austin, G. J. O. Beran, Y. A. Bernard, E. Berquist, K. Brandhorst, K. B. Bravaya, S. T. Brown, D. Casanova, C.-M. Chang, Y. Chen, S. H. Chien, K. D. Closser, D. L. Crittenden, M. Diedenhofen, R. A. D. Jr., H. Do, A. D. Dutoi, R. G. Edgar, S. Fatehi, L. Fusti-Molnar, A. Ghysels, A. Golubeva-Zadorozhnaya, J. Gomes, M. W. Hanson-Heine, P. H. Harbach, A. W. Hauser, E. G. Hohenstein, Z. C. Holden, T.-C. Jagau, H. Ji, B. Kaduk, K. Khistyaev, J. Kim, J. Kim, R. A. King, P. Klunzinger, D. Kosenkov, T. Kowalczyk, C. M. Krauter, K. U. Lao, A. D. Laurent, K. V. Lawler, S. V. Levchenko, C. Y. Lin, F. Liu, E. Livshits, R. C. Lochan, A. Luenser, P. Manohar, S. F. Manzer, S.-P. Mao, N. Mardirossian, A. V. Marenich, S. A. Maurer, N. J. Mayhall, E. Neuscamman, C. M. Oana, R. Olivares-Amaya, D. P. O'Neill, J. A. Parkhill, T. M. Perrine, R. Peverati, A. Prociuk, D. R. Rehn, E. Rosta, N. J. Russ, S. M. Sharada, S. Sharma, D. W. Small, A. Sodt, T. Stein, D. Stück, Y.-C. Su, A. J. Thom, T. Tsuchimochi, V. Vanovschi, L. Vogt, O. Vydrov, T. Wang, M. A. Watson, J. Wenzel, A. White, C. F. Williams, J. Yang, S. Yeganeh, S. R. Yost, Z.-Q. You, I. Y. Zhang, X. Zhang, Y. Zhao, B. R. Brooks, G. K. Chan, D. M. Chipman, C. J. Cramer, W. A. Goddard III, M. S. Gordon, W. J. Hehre, A. Klamt, H. F. Schaefer III, M. W. Schmidt, C. D. Sherrill, D. G. Truhlar, A. Warshel, X. Xu, A. Aspuru-Guzik, R. Baer, A. T. Bell, N. A. Besley, J.-D. Chai, A. Dreuw, B. D. Dunietz, T. R. Furlani, S. R. Gwaltney, C.-P. Hsu, Y. Jung, J. Kong, D. S. Lambrecht, W. Liang, C. Ochsenfeld, V. A. Rassolov, L. V. Slipchenko, J. E. Subotnik, T. V. Voorhis, J. M. Herbert, A. I. Krylov, P. M. Gill and M. Head-Gordon, Molecular Physics, 113 (2) pp. 184-215 (2015). [DOI] [URL]

"Maturation of the HIV-1 core by a non-diffusional phase transition," G. A. Frank, K. Narayan, J. W. Bess Jr, G. Q. Del Prete, X. Wu, A. Moran, L. M. Hartnell, L. A. Earl, J. D. Lifson and S. Subramaniam, Nature Communications, 6 pp. 5854 EP 1-9 (2015). [URL]

"Development and implementation of (Q)SAR modeling within the CHARMMing web-user interface," I. E. Weidlich, Y. Pevzner, B. T. Miller, I. V. Filippov, H. L. Woodcock and B. R. Brooks, Journal of Computational Chemistry, 36 (1) pp. 62-67 (2015). [DOI] [URL]

"Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations," G. König and B. R. Brooks, Biochimica et Biophysica Acta (BBA) - General Subjects, 1850 (5) pp. 932 - 943 (2015). [DOI] [URL]

"Conformational dynamics and aggregation behavior of piezoelectric diphenylalanine peptides in an external electric field," C. M. Kelly, T. Northey, K. Ryan, B. R. Brooks, A. L. Kholkin, B. J. Rodriguez and N.-V. Buchete, Biophysical Chemistry, 196 pp. 16 - 24 (2015). [DOI] [URL]

"Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest," J. Lee, K. Lee, I. Joung, K. Joo, B. R. Brooks and J. Lee, BMC Bioinformatics, 16 (1) pp. 94 (2015). [DOI] [URL]

"Comparative phosphoproteomic analysis of mammalian glomeruli reveals conserved podocin C-terminal phosphorylation as a determinant of slit diaphragm complex architecture," M. M. Rinschen, C. Pahmeyer, T. Pisitkun, N. Schnell, X. Wu, M. Maaβ, M. P. Bartram, T. Lamkemeyer, B. Schermer, T. Benzing and P. T. Brinkkoetter, PROTEOMICS, 15 (7) pp. 1326-1331 (2015). [DOI] [URL]

"Protein structure determination by conformational space annealing using NMR geometric restraints," K. Joo, I. Joung, J. Lee, J. Lee, W. Lee, B. Brooks, S. J. Lee and J. Lee, Proteins: Structure, Function, and Bioinformatics, 83 (12) pp. 2251-2262 (2015). [DOI] [URL]

2014

"Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial," B. T. Miller, R. P. Singh, V. Schalk, Y. Pevzner, J. Sun, C. S. Miller, S. Boresch, T. Ichiye, B. R. Brooks and H. L. Woodcock III, PLOS Computational Biology, 10 (7) pp. 1-7 (2014). [DOI] [URL]

"Web-Based Computational Chemistry Education with CHARMMing II: Coarse-Grained Protein Folding," F. C. Pickard IV, B. T. Miller, V. Schalk, M. G. Lerner, H. L. Woodcock III and B. R. Brooks, PLOS Computational Biology, 10 (7) pp. 1-7 (2014). [DOI] [URL]

"Web-Based Computational Chemistry Education with CHARMMing III: Reduction Potentials of Electron Transfer Proteins," B. S. Perrin Jr, B. T. Miller, V. Schalk, H. L. Woodcock, B. R. Brooks and T. Ichiye, PLOS Computational Biology, 10 (7) pp. 1-6 (2014). [DOI] [URL]

"Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes," G. König, P. S. Hudson, S. Boresch and H. L. Woodcock, Journal of Chemical Theory and Computation, 10 (4) pp. 1406-1419 (2014). [DOI] [URL]

"Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange," J. Lee, B. T. Miller, A. Damjanović and B. R. Brooks, Journal of Chemical Theory and Computation, 10 (7) pp. 2738-2750 (2014). [DOI] [URL]

"Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics," P. Tao, A. J. Sodt, Y. Shao, G. König and B. R. Brooks, Journal of Chemical Theory and Computation, 10 (10) pp. 4198-4207 (2014). [DOI] [URL]

"An efficient algorithm for multipole energies and derivatives based on spherical harmonics and extensions to particle mesh Ewald," A. C. Simmonett, F. C. Pickard IV, H. F. Schaefer III and B. R. Brooks, The Journal of Chemical Physics, 140 (18) pp. 184101 (2014). [DOI] [URL]

"Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4," G. König, F. C. Pickard IV, Y. Mei and B. R. Brooks, Journal of Computer-Aided Molecular Design, 28 (3) pp. 245-257 (2014). [DOI] [URL]

"Phosphoproteomic Analysis Reveals Regulatory Mechanisms at the Kidney Filtration Barrier," M. M. Rinschen, X. Wu, T. König, T. Pisitkun, H. Hagmann, C. Pahmeyer, T. Lamkemeyer, P. Kohli, N. Schnell, B. Schermer, S. Dryer, B. R. Brooks, P. Beltrao, M. Krueger, P. T. Brinkkoetter and T. Benzing, Journal of the American Society of Nephrology, 25 (7) pp. 1509-1522 (2014). [DOI] [URL]

2013

"Generating Reservoir Conformations for Replica Exchange through the Use of the Conformational Space Annealing Method," A. Okur, B. T. Miller, K. Joo, J. Lee and B. R. Brooks, Journal of Chemical Theory and Computation, 9 (2) pp. 1115-1124 (2013). [DOI] [URL]

"Protein-Protein Docking Using EMAP in CHARMM and Support Vector Machine: Application to Ab/Ag Complexes," J. D. Wright, K. Sargsyan, X. Wu, B. R. Brooks and C. Lim, Journal of Chemical Theory and Computation, 9 (9) pp. 4186-4194 (2013). [DOI] [URL]

"Understanding the basis of a class of paradoxical mutations in AraC through simulations," A. Damjanović, B. T. Miller and R. Schleif, Proteins: Structure, Function, and Bioinformatics, 81 (3) pp. 490-498 (2013). [DOI] [URL]

"Targeted conformational search with map-restrained self-guided Langevin dynamics: Application to flexible fitting into electron microscopic density maps," X. Wu, S. Subramaniam, D. A. Case, K. W. Wu and B. R. Brooks, Journal of Structural Biology, 183 (3) pp. 429 - 440 (2013). [DOI] [URL]

"Accurate High-Throughput Structure Mapping and Prediction with Transition Metal Ion FRET," X. Yu, X. Wu, G. Bermejo, B. Brooks and J. Taraska, Structure, 21 (1) pp. 9 - 19 (2013). [DOI] [URL]

2012

"Implementation of the force decomposition machine for molecular dynamics simulations," U. Borštnik, B. T. Miller, B. R. Brooks and D. Janežič, Journal of Molecular Graphics and Modelling, 38 pp. 243 - 247 (2012). [DOI] [URL]

"Correlating Protein Hot Spot Surface Analysis Using ProBiS with Simulated Free Energies of Protein-Protein Interfacial Residues," N. Carl, M. Hodošček, B. Vehar, J. Konc, B. R. Brooks and D. Janežič, Journal of Chemical Information and Modeling, 52 (10) pp. 2541-2549 (2012). [DOI] [URL]

"Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett's Acceptance Ratio and Enveloping Distribution Sampling Methods," G. König, B. T. Miller, S. Boresch, X. Wu and B. R. Brooks, Journal of Chemical Theory and Computation, 8 (10) pp. 3650-3662 (2012). [DOI] [URL]

"Comparison of Three Chain-of-States Methods: Nudged Elastic Band and Replica Path with Restraints or Constraints," P. Tao, M. Hodošček, J. D. Larkin, Y. Shao and B. R. Brooks, Journal of Chemical Theory and Computation, 8 (12) pp. 5035-5051 (2012). [DOI] [URL]

"Effects of pH on Proteins: Predictions for Ensemble and Single-Molecule Pulling Experiments," E. P. O'Brien, B. R. Brooks and D. Thirumalai, Journal of the American Chemical Society, 134 (2) pp. 979-987 (2012). [DOI] [URL]

"Quantum Chemical Study of the Ground and Excited State Electronic Structures of Carbazole Oligomers with and without Triarylborane Substitutes," S. Zhang, Z. Qu, P. Tao, B. Brooks, Y. Shao, X. Chen and C. Liu, The Journal of Physical Chemistry C, 116 (23) pp. 12434-12442 (2012). [DOI] [URL]

"Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling," X. Wu, M. Hodošček and B. R. Brooks, The Journal of Chemical Physics, 137 (4) pp. 044106 (2012). [DOI] [URL]

"Maintain rigid structures in Verlet based Cartesian molecular dynamics simulations," P. Tao, X. Wu and B. R. Brooks, The Journal of Chemical Physics, 137 (13) pp. 134110 (2012). [DOI] [URL]

"Weak Intra-Ring Allosteric Communications of the Archaeal Chaperonin Thermosome Revealed by Normal Mode Analysis," M. Jayasinghe, P. Shrestha, X. Wu, R. Tehver and G. Stan, Biophysical Journal, 103 (6) pp. 1285 - 1295 (2012). [DOI] [URL]

"Simulation of multiphase systems utilizing independent force fields to control intraphase and interphase behavior," P. K. Biswas, N. A. Vellore, J. A. Yancey, T. G. Kucukkal, G. Collier, B. R. Brooks, S. J. Stuart and R. A. Latour, Journal of Computational Chemistry, 33 (16) pp. 1458-1466 (2012). [DOI] [URL]

"Comparing normal modes across different models and scales: Hessian reduction versus coarse-graining," A. Ghysels, B. T. Miller, F. C. Pickard IV and B. R. Brooks, Journal of Computational Chemistry, 33 (28) pp. 2250-2275 (2012). [DOI] [URL]

"Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations," G. König and B. R. Brooks, Journal of Computer-Aided Molecular Design, 26 (5) pp. 543-550 (2012). [DOI] [URL]

"MDMS: Molecular dynamics meta-simulator for evaluating exchange type sampling methods," D. B. Smith, A. Okur and B. R. Brooks, Chemical Physics Letters, 545 pp. 118 - 124 (2012). [DOI] [URL]

"Reaction path optimization and sampling methods and their applications for rare events," P. Tao, B. R. Brooks and J. D. Larkin, , In Some Applications of Quantum Mechanics. pp. 27-66 INTECH Open Access Publisher. (2012). [DOI] [URL]

"Molecular simulation with discrete fast fourier transform," X. Wu and B. R. Brooks, , In Fourier Transform - Materials Analysis. pp. 137-164 INTECH Open Access Publisher. (2012). [DOI] [URL]

"Efficient and Unbiased Sampling of Biomolecular Systems in the Canonical Ensemble: A Review of Self-Guided Langevin Dynamics," X. Wu, A. Damjanović and B. R. Brooks, , In Advances in Chemical Physics. pp. 255-326 John Wiley & Sons, Inc.. (2012). [DOI] [URL]

"A Common Molecular Basis for Exogenous and Endogenous Cannabinoid Potentiation of Glycine Receptors," W. Xiong, X. Wu, D. M. Lovinger and L. Zhang, Journal of Neuroscience, 32 (15) pp. 5200-5208 (2012). [DOI] [URL]

2011

"Efficient Calculation of QM/MM Frequencies with the Mobile Block Hessian," A. Ghysels, H. L. Woodcock, J. D. Larkin, B. T. Miller, Y. Shao, J. Kong, D. V. Neck, V. V. Speybroeck, M. Waroquier and B. R. Brooks, Journal of Chemical Theory and Computation, 7 (2) pp. 496-514 (2011). [DOI] [URL]

"MSCALE: A General Utility for Multiscale Modeling," H. L. Woodcock, B. T. Miller, M. Hodošček, A. Okur, J. D. Larkin, J. W. Ponder and B. R. Brooks, Journal of Chemical Theory and Computation, 7 (4) pp. 1208-1219 (2011). [DOI] [URL]

"Conformational Relaxation and Water Penetration Coupled to Ionization of Internal Groups in Proteins," A. Damjanović, B. R. Brooks and B. García-Moreno E., The Journal of Physical Chemistry A, 115 (16) pp. 4042-4053 (2011). [DOI] [URL]

"Influence of Nanoparticle Size and Shape on Oligomer Formation of an Amyloidogenic Peptide," E. P. O'Brien, J. E. Straub, B. R. Brooks and D. Thirumalai, The Journal of Physical Chemistry Letters, 2 (10) pp. 1171-1177 (2011). [DOI] [URL]

"Toward canonical ensemble distribution from self-guided Langevin dynamics simulation," X. Wu and B. R. Brooks, The Journal of Chemical Physics, 134 (13) pp. 134108 (2011). [DOI] [URL]

"Force-momentum-based self-guided Langevin dynamics: A rapid sampling method that approaches the canonical ensemble," X. Wu and B. R. Brooks, The Journal of Chemical Physics, 135 (20) pp. 204101 (2011). [DOI] [URL]

"Extracellular Complexes of the Hematopoietic Human and Mouse CSF-1 Receptor Are Driven by Common Assembly Principles," J. Elegheert, A. Desfosses, A. Shkumatov, X. Wu, N. Bracke, K. Verstraete, K. V. Craenenbroeck, B. Brooks, D. Svergun, B. Vergauwen, I. Gutsche and S. Savvides, Structure, 19 (12) pp. 1762 - 1772 (2011). [DOI] [URL]

"The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations," U. Borštnik, B. T. Miller, B. R. Brooks and D. Janežič, Journal of Computational Chemistry, 32 (14) pp. 3005-3013 (2011). [DOI] [URL]

"Lateral density of receptor arrays in the membrane plane influences sensitivity of the E. coli chemotaxis response," C. M. Khursigara, G. Lan, S. Neumann, X. Wu, S. Ravindran, M. J. Borgnia, V. Sourjik, J. Milne, Y. Tu and S. Subramaniam, The EMBO Journal, 30 (9) pp. 1719-1729 (2011). [DOI] [URL]

"pH replica-exchange method based on discrete protonation states," S. G. Itoh, A. Damjanović and B. R. Brooks, Proteins: Structure, Function, and Bioinformatics, 79 (12) pp. 3420-3436 (2011). [DOI] [URL]

"Automatic Spot Identification for High Throughput Microarray Analysis," E. Wu, Y. A. Su, E. Billings, B. R. Brooks and X. Wu, Journal of Bioengineering & Biomedical Science, Suppl 5 (005) (2011). [DOI] [URL]

2010

"A Computational Investigation of the Nitrogen-Boron Interaction in o-(N,N-Dialkylaminomethyl)arylboronate Systems," J. D. Larkin, J. S. Fossey, T. D. James, B. R. Brooks and C. W. Bock, The Journal of Physical Chemistry A, 114 (47) pp. 12531-12539 (2010). [DOI] [URL]

"A parallel implementation of the analytic nuclear gradient for time-dependent density functional theory within the Tamm-Dancoff approximation," F. Liu, Z. Gan, Y. Shao, C.-P. Hsu, A. Dreuw, M. Head-Gordon, B. T. Miller, B. R. Brooks, J.-G. Yu, T. R. Furlani and J. Kong, Molecular Physics, 108 (19-20) pp. 2791-2800 (2010). [DOI] [URL]

"Comparative study of various normal mode analysis techniques based on partial Hessians," A. Ghysels, V. Van Speybroeck, E. Pauwels, S. Catak, B. R. Brooks, D. Van Neck and M. Waroquier, Journal of Computational Chemistry, 31 (5) pp. 994-1007 (2010). [DOI] [URL]

"Probing the Periplasmic-Open State of Lactose Permease in Response to Sugar Binding and Proton Translocation," P. Y. Pendse, B. R. Brooks and J. B. Klauda, Journal of Molecular Biology, 404 (3) pp. 506 - 521 (2010). [DOI] [URL]

2009

"Molecular Origin of Constant m-Values, Denatured State Collapse, and Residue-Dependent Transition Midpoints in Globular Proteins," E. P. O'Brien, B. R. Brooks and D. Thirumalai, Biochemistry, 48 (17) pp. 3743-3754 (2009). [DOI] [URL]

"Mobile Block Hessian Approach with Adjoined Blocks: An Efficient Approach for the Calculation of Frequencies in Macromolecules," A. Ghysels, V. Van Speybroeck, E. Pauwels, D. Van Neck, B. R. Brooks and M. Waroquier, Journal of Chemical Theory and Computation, 5 (5) pp. 1203-1215 (2009). [DOI] [URL]

"Computational Investigation of the Oxidative Deboronation of Boroglycine, H_2N−CH_2−B(OH)_2, Using H_2O and H_2O_2," J. D. Larkin, G. D. Markham, M. Milkevitch, B. R. Brooks and C. W. Bock, The Journal of Physical Chemistry A, 113 (41) pp. 11028-11034 (2009). [DOI] [URL]

"Thermodynamic Perspective on the Dock-Lock Growth Mechanism of Amyloid Fibrils," E. P. O'Brien, Y. Okamoto, J. E. Straub, B. R. Brooks and D. Thirumalai, The Journal of Physical Chemistry B, 113 (43) pp. 14421-14430 (2009). [DOI] [URL]

"Computational Validation of Protein Nanotubes," I. Buch, B. R. Brooks, H. J. Wolfson and R. Nussinov, Nano Letters, 9 (3) pp. 1096-1102 (2009). [DOI] [URL]

"Normal modes for large molecules with arbitrary link constraints in the mobile block Hessian approach," A. Ghysels, D. V. Neck, B. R. Brooks, V. V. Speybroeck and M. Waroquier, The Journal of Chemical Physics, 130 (8) pp. 084107 (2009). [DOI] [URL]

"How accurate are polymer models in the analysis of Förster resonance energy transfer experiments on proteins?," E. P. O'Brien, G. Morrison, B. R. Brooks and D. Thirumalai, The Journal of Chemical Physics, 130 (12) pp. 124903 (2009). [DOI] [URL]

"Isotropic periodic sum of electrostatic interactions for polar systems," X. Wu and B. R. Brooks, The Journal of Chemical Physics, 131 (2) pp. 024107 (2009). [DOI] [URL]

"CHARMM: The biomolecular simulation program," B. R. Brooks, C. L. Brooks, A. D. Mackerell, L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodošček, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York and M. Karplus, Journal of Computational Chemistry, 30 (10) pp. 1545-1614 (2009). [DOI] [URL]

"Artificial reaction coordinate ''tunneling'' in free-energy calculations: The catalytic reaction of RNase H," E. Rosta, H. L. Woodcock, B. R. Brooks and G. Hummer, Journal of Computational Chemistry, 30 (11) pp. 1634-1641 (2009). [DOI] [URL]

"Binding and release of cholesterol in the Osh4 protein of yeast," R. P. Singh, B. R. Brooks and J. B. Klauda, Proteins: Structure, Function, and Bioinformatics, 75 (2) pp. 468-477 (2009). [DOI] [URL]

"Self-guided Langevin dynamics study of regulatory interactions in NtrC," A. Damjanović, B. García-Moreno E. and B. R. Brooks, Proteins: Structure, Function, and Bioinformatics, 76 (4) pp. 1007-1019 (2009). [DOI] [URL]

"Highly parallel multi-dimensional fast fourier transform on fine-And coarse-grained many-core approaches," A. B. Saybasili, A. Tzannes, B. R. Brooks and U. Vishkin, , In Proceedings of the 21st IASTED International Conference. 668 (018) pp. 107 (2009). [URL]

"Allosteric Transitions in Biological Nanomachines are Described by Robust Normal Modes of Elastic Networks," W. Zheng, B. R. Brooks and D. Thirumalai, Current Protein and Peptide Science, 10 (2) pp. 128-132 (2009). [DOI] [URL]

2008

"Backbone Relaxation Coupled to the Ionization of Internal Groups in Proteins: A Self-Guided Langevin Dynamics Study," A. Damjanović, X. Wu, E. Bertrand García-Moreno and B. R. Brooks, Biophysical Journal , 95 (9) pp. 4091 - 4101 (2008). [DOI] [URL]

"CHARMMing: A New, Flexible Web Portal for CHARMM," B. T. Miller, R. P. Singh, J. B. Klauda, M. Hodošček, B. R. Brooks and H. L. Woodcock, Journal of Chemical Information and Modeling, 48 (9) pp. 1920-1929 (2008). [DOI] [URL]

"Open Science Grid Study of the Coupling between Conformation and Water Content in the Interior of a Protein," A. Damjanović, B. T. Miller, T. J. Wenaus, P. Maksimović, B. García-Moreno E. and B. R. Brooks, Journal of Chemical Information and Modeling, 48 (10) pp. 2021-2029 (2008). [DOI] [URL]

"CHARMM Force Field Parameters for Nitroalkanes and Nitroarenes," J. B. Klauda and B. R. Brooks, Journal of Chemical Theory and Computation, 4 (1) pp. 107-115 (2008). [DOI] [URL]

"Pathways and Populations: Stereoelectronic Insights into the Exocyclic Torsion of 5-(Hydroxymethyl)tetrahydropyran," H. L. Woodcock, B. R. Brooks and R. W. Pastor, Journal of the American Chemical Society, 130 (20) pp. 6345-6347 (2008). [DOI] [URL]

"Collective and Noncollective Models of NMR Relaxation in Lipid Vesicles and Multilayers," J. B. Klauda, N. V. Eldho, K. Gawrisch, B. R. Brooks and R. W. Pastor, The Journal of Physical Chemistry B, 112 (19) pp. 5924-5929 (2008). [DOI] [URL]

"Dimers of Boroglycine and Methylamine Boronic Acid: A Computational Comparison of the Relative Importance of Dative versus Hydrogen Bonding," J. D. Larkin, M. Milkevitch, K. L. Bhat, G. D. Markham, B. R. Brooks and C. W. Bock, The Journal of Physical Chemistry A, 112 (1) pp. 125-133 (2008). [DOI] [URL]

"Langevin Network Model of Myosin," B. T. Miller, W. Zheng, R. M. Venable, R. W. Pastor and B. R. Brooks, The Journal of Physical Chemistry B, 112 (19) pp. 6274-6281 (2008). [DOI] [URL]

"Molecular Dynamics Simulations of Perylene and Tetracene Librations: Comparison With Femtosecond Upconversion Data," T. Rosales, J. Xu, X. Wu, M. Hodošček, P. Callis, B. R. Brooks and J. R. Knutson, The Journal of Physical Chemistry A, 112 (25) pp. 5593-5597 (2008). [DOI] [URL]

"A Computational Characterization of Boron-Oxygen Multiple Bonding in HN=CH-CH=CH-NH-BO," J. D. Larkin, K. L. Bhat, G. D. Markham, T. D. James, B. R. Brooks and C. W. Bock, The Journal of Physical Chemistry A, 112 (36) pp. 8446-8454 (2008). [DOI] [URL]

"Factors Governing Helix Formation in Peptides Confined to Carbon Nanotubes," E. P. O'Brien, G. Stan, D. Thirumalai and B. R. Brooks, Nano Letters, 8 (11) pp. 3702-3708 (2008). [DOI] [URL]

"Using the isotropic periodic sum method to calculate long-range interactions of heterogeneous systems," X. Wu and B. R. Brooks, The Journal of Chemical Physics, 129 (15) pp. 154115 (2008). [DOI] [URL]

"Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit," H. L. Woodcock, W. Zheng, A. Ghysels, Y. Shao, J. Kong and B. R. Brooks, The Journal of Chemical Physics, 129 (21) pp. 214109 (2008). [DOI] [URL]

"Chemoreceptors in Caulobacter crescentus: Trimers of Receptor Dimers in a Partially Ordered Hexagonally Packed Array," C. M. Khursigara, X. Wu and S. Subramaniam, Journal of Bacteriology, 190 (20) pp. 6805-6810 (2008). [DOI] [URL]

"Role of HAMP domains in chemotaxis signaling by bacterial chemoreceptors," C. M. Khursigara, X. Wu, P. Zhang, J. Lefman and S. Subramaniam, Proceedings of the National Academy of Sciences, 105 (43) pp. 16555-16560 (2008). [DOI] [URL]

"Rotation of Lipids in Membranes: Molecular Dynamics Simulation, ^31P Spin-Lattice Relaxation, and Rigid-Body Dynamics," J. B. Klauda, M. F. Roberts, A. G. Redfield, B. R. Brooks and R. W. Pastor, Biophysical Journal, 94 (8) pp. 3074 - 3083 (2008). [DOI] [URL]

"Extended Polypeptide Linkers Establish the Spatial Architecture of a Pyruvate Dehydrogenase Multienzyme Complex," J. S. Lengyel, K. M. Stott, X. Wu, B. R. Brooks, A. Balbo, P. Schuck, R. N. Perham, S. Subramaniam and J. L. Milne, Structure, 16 (1) pp. 93 - 103 (2008). [DOI] [URL]

"Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model," E. P. O'Brien, G. Ziv, G. Haran, B. R. Brooks and D. Thirumalai, Proceedings of the National Academy of Sciences, 105 (36) pp. 13403-13408 (2008). [DOI] [URL]

"A new model defines the minimal set of polymorphism in HLA-DQ and -DR that determines susceptibility and resistance to autoimmune diabetes," C. S. Parry and B. R. Brooks, Biology Direct, 3 (1) pp. 42 (2008). [DOI] [URL]

"Multiscale methods for macromolecular simulations," P. Sherwood, B. R. Brooks and M. S. Sansom, Current Opinion in Structural Biology, 18 (5) pp. 630 - 640 (2008). [DOI] [URL]

2007

"Protein recognition motifs: Design of peptidomimetics of helix surfaces," Y. Che, B. R. Brooks and G. R. Marshall, Biopolymers, 86 (4) pp. 288-297 (2007). [DOI] [URL]

"Engineering Metal Complexes of Chiral Pentaazacrowns as Privileged Reverse-turn Scaffolds," Y. Che, B. R. Brooks, D. P. Riley, A. J. H. Reaka and G. R. Marshall, Chemical Biology & Drug Design, 69 (2) pp. 99-110 (2007). [DOI] [URL]

"Carbene Stabilization by Aryl Substituents. Is Bigger Better?," H. L. Woodcock, D. Moran, B. R. Brooks, P. v. R. Schleyer and H. F. Schaefer, Journal of the American Chemical Society, 129 (12) pp. 3763-3770 (2007). [DOI] [URL]

"Interactions between Hydrophobic and Ionic Solutes in Aqueous Guanidinium Chloride and Urea Solutions: Lessons for Protein Denaturation Mechanism," E. P. O'Brien, R. I. Dima, B. Brooks and D. Thirumalai, Journal of the American Chemical Society, 129 (23) pp. 7346-7353 (2007). [DOI] [URL]

"Long-Range Lennard-Jones and Electrostatic Interactions in Interfaces: Application of the Isotropic Periodic Sum Method," J. B. Klauda, X. Wu, R. W. Pastor and B. R. Brooks, The Journal of Physical Chemistry B, 111 (17) pp. 4393-4400 (2007). [DOI] [URL]

"A Computational Investigation of the Geometrical Structure and Protodeboronation of Boroglycine, H2N-CH2-B(OH)2," J. D. Larkin, K. L. Bhat, G. D. Markham, B. R. Brooks, J. H. Lai and C. W. Bock, The Journal of Physical Chemistry A, 111 (28) pp. 6489-6500 (2007). [DOI] [URL]

"Exploring SCC-DFTB Paths for Mapping QM/MM Reaction Mechanisms," H. L. Woodcock, M. Hodošček and B. R. Brooks, The Journal of Physical Chemistry A, 111 (26) pp. 5720-5728 (2007). [DOI] [URL]

"Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations," H. L. Woodcock, M. Hodošček, A. T. B. Gilbert, P. M. W. Gill, H. F. Schaefer and B. R. Brooks, Journal of Computational Chemistry, 28 (9) pp. 1485-1502 (2007). [DOI] [URL]

"Sugar Binding in Lactose Permease: Anomeric State of a Disaccharide Influences Binding Structure," J. B. Klauda and B. R. Brooks, Journal of Molecular Biology, 367 (5) pp. 1523 - 1534 (2007). [DOI] [URL]

"Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model," W. Zheng, J.-C. Liao, B. R. Brooks and S. Doniach, Proteins: Structure, Function, and Bioinformatics, 67 (4) pp. 886-896 (2007). [DOI] [URL]

"Protein conformational transitions explored by mixed elastic network models," W. Zheng, B. R. Brooks and G. Hummer, Proteins: Structure, Function, and Bioinformatics, 69 (1) pp. 43-57 (2007). [DOI] [URL]

"Coupling between allosteric transitions in GroEL and assisted folding of a substrate protein," G. Stan, G. H. Lorimer, D. Thirumalai and B. R. Brooks, Proceedings of the National Academy of Sciences, 104 (21) pp. 8803-8808 (2007). [DOI] [URL]

"Ab Initio Modeling of Glycosyl Torsions and Anomeric Effects in a Model Carbohydrate: 2-Ethoxy Tetrahydropyran," H. L. Woodcock, D. Moran, R. W. Pastor, A. D. M. Jr. and B. R. Brooks, Biophysical Journal, 93 (1) pp. 1 - 10 (2007). [DOI] [URL]

"Allosteric Transitions in the Chaperonin GroEL are Captured by a Dominant Normal Mode that is Most Robust to Sequence Variations," W. Zheng, B. R. Brooks and D. Thirumalai, Biophysical Journal, 93 (7) pp. 2289 - 2299 (2007). [DOI] [URL]

2006

"Development of small molecules designed to modulate protein-protein interactions," Y. Che, B. R. Brooks and G. R. Marshall, Journal of Computer-Aided Molecular Design, 20 (2) pp. 109-130 (2006). [DOI] [URL]

"Structure of the Boronic Acid Dimer and the Relative Stabilities of Its Conformers," J. D. Larkin, K. L. Bhat, G. D. Markham, B. R. Brooks, H. F. Schaefer and C. W. Bock, The Journal of Physical Chemistry A, 110 (36) pp. 10633-10642 (2006). [DOI] [URL]

"Dynamical motions of lipids and a finite size effect in simulations of bilayers," J. B. Klauda, B. R. Brooks and R. W. Pastor, The Journal of Chemical Physics, 125 (14) pp. 144710-1-8 (2006). [DOI] [URL]

"Simulation-Based Methods for Interpreting X-Ray Data from Lipid Bilayers," J. B. Klauda, N. Kučerka, B. R. Brooks, R. W. Pastor and J. F. Nagle, Biophysical Journal, 90 (8) pp. 2796 - 2807 (2006). [DOI] [URL]

"Molecular Structure of a 9-MDa Icosahedral Pyruvate Dehydrogenase Subcomplex Containing the E2 and E3 Enzymes Using Cryoelectron Microscopy," J. L. S. Milne, X. Wu, M. J. Borgnia, J. S. Lengyel, B. R. Brooks, D. Shi, R. N. Perham and S. Subramaniam, Journal of Biological Chemistry, 281 (7) pp. 4364-4370 (2006). [DOI] [URL]

"Residues in substrate proteins that interact with GroEL in the capture process are buried in the native state," G. Stan, B. R. Brooks, G. H. Lorimer and D. Thirumalai, Proceedings of the National Academy of Sciences of the United States of America, 103 (12) pp. 4433-4438 (2006). [DOI] [URL]

"Temperature dependence of diffusion properties of soft sticky dipole water," M.-L. Tan, B. R. Brooks and T. Ichiye, Chemical Physics Letters, 421 (1-3) pp. 166 - 170 (2006). [DOI] [URL]

"Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations," W. Zheng, B. R. Brooks and D. Thirumalai, Proceedings of the National Academy of Sciences, 103 (20) pp. 7664-7669 (2006). [DOI] [URL]

"Modeling Protein Conformational Changes by Iterative Fitting of Distance Constraints Using Reoriented Normal Modes," W. Zheng and B. R. Brooks, Biophysical Journal, 90 (12) pp. 4327 - 4336 (2006). [DOI] [URL]

2005

"An ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer," J. B. Klauda, B. R. Brooks, A. D. MacKerell, R. M. Venable and R. W. Pastor, The Journal of Physical Chemistry B, 109 (11) pp. 5300-5311 (2005). [DOI] [URL]

"Adjacent Gauche Stabilization in Linear Alkanes: Implications for Polymer Models and Conformational Analysis," J. B. Klauda, R. W. Pastor and B. R. Brooks, The Journal of Physical Chemistry B, 109 (33) pp. 15684-15686 (2005). [DOI] [URL]

"Isotropic periodic sum: A method for the calculation of long-range interactions," X. Wu and B. R. Brooks, The Journal of Chemical Physics, 122 (4) pp. 044107-1-18 (2005). [DOI] [URL]

"Identifying natural substrates for chaperonins using a sequence-based approach," G. Stan, B. R. Brooks, G. H. Lorimer and D. Thirumalai, Protein Science, 14 (1) pp. 193-201 (2005). [DOI] [URL]

"Probing the ''Annealing'' Mechanism of GroEL Minichaperone using Molecular Dynamics Simulations," G. Stan, B. R. Brooks and D. Thirumalai, Journal of Molecular Biology, 350 (4) pp. 817 - 829 (2005). [DOI] [URL]

"Probing the Local Dynamics of Nucleotide-Binding Pocket Coupled to the Global Dynamics: Myosin versus Kinesin," W. Zheng and B. R. Brooks, Biophysical Journal, 89 (1) pp. 167 - 178 (2005). [DOI] [URL]

"Normal-Modes-Based Prediction of Protein Conformational Changes Guided by Distance Constraints," W. Zheng and B. R. Brooks, Biophysical Journal, 88 (5) pp. 3109 - 3117 (2005). [DOI] [URL]

"Network of Dynamically Important Residues in the Open/Closed Transition in Polymerases Is Strongly Conserved," W. Zheng, B. R. Brooks, S. Doniach and D. Thirumalai, Structure, 13 (4) pp. 565 - 577 (2005). [DOI] [URL]

"Identification of Dynamical Correlations within the Myosin Motor Domain by the Normal Mode Analysis of an Elastic Network Model," W. Zheng and B. Brooks, Journal of Molecular Biology, 346 (3) pp. 745 - 759 (2005). [DOI] [URL]

2004

"A comprehensive picture of non-site specific oxidation of methionine residues by peroxides in protein pharmaceuticals," J. Chu, J. Yin, B. R. Brooks, D. I. Wang, M. S. Ricci, D. N. Brems and B. L. Trout, Journal of Pharmaceutical Sciences, 93 (12) pp. 3096 - 3102 (2004). [DOI] [URL]

"Oxidation of Methionine Residues in Aqueous Solutions: Free Methionine and Methionine in Granulocyte Colony-Stimulating Factor," J.-W. Chu, B. R. Brooks and B. L. Trout, Journal of the American Chemical Society, 126 (50) pp. 16601-16607 (2004). [DOI] [URL]

"Pressure-Based Long-Range Correction for Lennard-Jones Interactions in Molecular Dynamics Simulations: Application to Alkanes and Interfaces," P. Lagüe, R. W. Pastor and B. R. Brooks, The Journal of Physical Chemistry B, 108 (1) pp. 363-368 (2004). [DOI] [URL]

"The Local Maximum Clustering Method and Its Application in Microarray Gene Expression Data Analysis," X. Wu, Y. Chen, B. R. Brooks and Y. A. Su, EURASIP Journal on Advances in Signal Processing, 2004 (1) pp. 53-63 (2004). [DOI] [URL]

"β-Hairpin Folding Mechanism of a Nine-Residue Peptide Revealed from Molecular Dynamics Simulations in Explicit Water," X. Wu and B. R. Brooks, Biophysical Journal, 86 (4) pp. 1946 - 1958 (2004). [DOI] [URL]

2003

"A super-linear minimization scheme for the nudged elastic band method," J.-W. Chu, B. L. Trout and B. R. Brooks, The Journal of Chemical Physics, 119 (24) pp. 12708-12717 (2003). [DOI] [URL]

"An improved method for nonbonded list generation: Rapid determination of near-neighbor pairs," R. J. Petrella, I. Andricioaei, B. R. Brooks and M. Karplus, Journal of Computational Chemistry, 24 (2) pp. 222-231 (2003). [DOI] [URL]

"Exploring the quantum mechanical/molecular mechanical replica path method: a pathway optimization of the chorismate to prephenate Claisen rearrangement catalyzed by chorismate mutase," H. Lee Woodcock, M. Hodošček, P. Sherwood, Y. S. Lee, H. F. Schaefer III and B. R. Brooks, Theoretical Chemistry Accounts, 109 (3) pp. 140-148 (2003). [DOI] [URL]

"A temperature of maximum density in soft sticky dipole water," M.-L. Tan, J. T. Fischer, A. Chandra, B. R. Brooks and T. Ichiye, Chemical Physics Letters, 376 (5-6) pp. 646 - 652 (2003). [DOI] [URL]

"Self-guided Langevin dynamics simulation method," X. Wu and B. R. Brooks, Chemical Physics Letters, 381 (3-4) pp. 512 - 518 (2003). [DOI] [URL]

"A core-weighted fitting method for docking atomic structures into low-resolution maps: Application to cryo-electron microscopy," X. Wu, J. L. Milne, M. J. Borgnia, A. V. Rostapshov, S. Subramaniam and B. R. Brooks, Journal of Structural Biology, 141 (1) pp. 63 - 76 (2003). [DOI] [URL]

2002

"An Ab Initio Study of Amide Proton Shift Tensor Dependence on Local Protein Structure," Y. Sharma, O. Y. Kwon, B. Brooks and N. Tjandra, Journal of the American Chemical Society, 124 (2) pp. 327-335 (2002). [DOI] [URL]

"Hydrogen Bonding in High-Resolution Protein Structures: A New Method To Assess NMR Protein Geometry," R. S. Lipsitz, Y. Sharma, B. R. Brooks and N. Tjandra, Journal of the American Chemical Society, 124 (35) pp. 10621-10626 (2002). [DOI] [URL]

"Direct Observation of the Folding and Unfolding of a β-Hairpin in Explicit Water through Computer Simulation," X. Wu, S. Wang and B. R. Brooks, Journal of the American Chemical Society, 124 (19) pp. 5282-5283 (2002). [DOI] [URL]

"Reaction Mechanism of Chorismate Mutase Studied by the Combined Potentials of Quantum Mechanics and Molecular Mechanics," Y. S. Lee, S. E. Worthington, M. Krauss and B. R. Brooks, The Journal of Physical Chemistry B, 106 (46) pp. 12059-12065 (2002). [DOI] [URL]

"Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method," D. Das, K. P. Eurenius, E. M. Billings, P. Sherwood, D. C. Chatfield, M. Hodošček and B. R. Brooks, The Journal of Chemical Physics, 117 (23) pp. 10534-10547 (2002). [DOI] [URL]

"Simulations of Membranes and Other Interfacial Systems Using P21\ and Pc Periodic Boundary Conditions," E. A. Dolan, R. M. Venable, R. W. Pastor and B. R. Brooks, Biophysical Journal, 82 (5) pp. 2317 - 2325 (2002). [DOI] [URL]

"Molecular architecture and mechanism of an icosahedral pyruvate dehydrogenase complex: a multifunctional catalytic machine," J. L. Milne, D. Shi, P. B. Rosenthal, J. S. Sunshine, G. J. Domingo, X. Wu, B. R. Brooks, R. N. Perham, R. Henderson and S. Subramaniam, The EMBO Journal, 21 (21) pp. 5587-5598 (2002). [DOI] [URL]

"Annealing function of GroEL: structural and bioinformatic analysis," G. Stan, D. Thirumalai, G. H. Lorimer and B. R. Brooks, Biophysical Chemistry, 100 (1-3) pp. 453 - 467 (2002). [DOI] [URL]

2001

"Molecular Modeling of Nucleic Acid Structure," T. E. Cheatham III, B. R. Brooks and P. A. Kollman, , In Current Protocols in Nucleic Acid Chemistry. pp. UNIT 7.5 John Wiley & Sons, Inc.. (2001). [DOI] [URL]

"Molecular Dynamics Simulations of Human Rhinovirus and an Antiviral Compound," B. Speelman, B. R. Brooks and C. B. Post, Biophysical Journal, 80 (1) pp. 121 - 129 (2001). [DOI] [URL]

2000

"Elastic molecular dynamics with self-consistent flexible constraints," J. Zhou, S. Reich and B. R. Brooks, The Journal of Chemical Physics, 112 (18) pp. 7919-7929 (2000). [DOI] [URL]

1998

"HIV-1 protease cleavage mechanism: A theoretical investigation based on classical MD\ simulation and reaction path calculations using a hybrid QM/MM potential," D. C. Chatfield, K. P. Eurenius and B. R. Brooks, Journal of Molecular Structure: THEOCHEM\, 423 (1-2) pp. 79 - 92 (1998). [DOI] [URL]

"Recent advances in molecular dynamics simulation towards the realistic representation of biomolecules in solution," T. E. Cheatham III and B. R. Brooks, Theoretical Chemistry Accounts, 99 (5) pp. 279-288 (1998). [DOI] [URL]

"Molecular Dynamics of Staphylococcal Nuclease: Comparison of Simulation with ^15N and ^13C NMR Relaxation Data," D. C. Chatfield, A. Szabo and B. R. Brooks, Journal of the American Chemical Society, 120 (21) pp. 5301-5311 (1998). [DOI] [URL]

"Alternate Pathways for Acetic Acid and Acetate ion Release from Acetylcholinesterase: a Molecular Dynamics Study," I. J. Enyedy, I. M. Kovach and B. R. Brooks, Journal of the American Chemical Society, 120 (32) pp. 8043-8050 (1998). [DOI] [URL]

"Removal of pressure and free energy artifacts in charged periodic systems via net charge corrections to the Ewald potential," S. Bogusz, III Thomas E. Cheatham and B. R. Brooks, The Journal of Chemical Physics, 108 (17) pp. 7070-7084 (1998). [DOI] [URL]

"Catalytic mechanism of aldose reductase studied by the combined potentials of quantum mechanics and molecular mechanics," Y. S. Lee, M. Hodošček, B. R. Brooks and P. F. Kador, Biophysical Chemistry, 70 (3) pp. 203 - 216 (1998). [DOI] [URL]

1997

"Structures of some substituted nitrophenols determined by ab initio computation on the origin of heterocliticity in anti-nitrophenol antibodies," C. S. Parry, B. R. Brooks, N. Matsunaga and L. Amzel, Journal of Molecular Structure: THEOCHEM, 398-399 pp. 555 - 563 (1997). [DOI] [URL]

1996

"Positioning of positively charged residues in the V3 loop correlates with HIV type 1 syncytium-inducing phenotype," D. Bhattacharyya, B. R. Brooks and L. Callahan, AIDS research and human retroviruses, 12 (2) pp. 83-90 (1996). [DOI] [URL]

"Effect of Electrostatic Force Truncation on Interfacial and Transport Properties of Water," S. E. Feller, R. W. Pastor, A. Rojnuckarin, S. Bogusz and B. R. Brooks, The Journal of Physical Chemistry, 100 (42) pp. 17011-17020 (1996). [DOI] [URL]

"Enzyme mechanisms with hybrid quantum and molecular mechanical potentials. I. Theoretical considerations," K. P. Eurenius, D. C. Chatfield, B. R. Brooks and M. Hodošček, International Journal of Quantum Chemistry, 60 (6) pp. 1189-1200 (1996). [DOI] [URL]

"Hydrated myoglobin's anharmonic fluctuations are not primarily due to dihedral transitions," P. J. Steinbach and B. R. Brooks, Proceedings of the National Academy of Sciences, 93 (1) pp. 55-59 (1996). [URL]

1995

"HIV-1 Protease Cleavage Mechanism Elucidated with Molecular Dynamics Simulation," D. C. Chatfield and B. R. Brooks, Journal of the American Chemical Society, 117 (20) pp. 5561-5572 (1995). [DOI] [URL]

"Computer simulation of liquid/liquid interfaces. I. Theory and application to octane/water," Y. Zhang, S. E. Feller, B. R. Brooks and R. W. Pastor, The Journal of Chemical Physics, 103 (23) pp. 10252-10266 (1995). [DOI] [URL]

"Constant pressure molecular dynamics simulation: The Langevin piston method," S. E. Feller, Y. Zhang, R. W. Pastor and B. R. Brooks, The Journal of Chemical Physics, 103 (11) pp. 4613-4621 (1995). [DOI] [URL]

"Parallelizing Molecular Dynamics Programs for Distributed-Memory Machines," Y.-S. Hwang, R. Das, J. H. Saltz, M. Hodošček and B. R. Brooks, IEEE Comput. Sci. Eng., 2 (2) pp. 18-29 (1995). [DOI] [URL]

"Harmonic analysis of large systems. I. Methodology," B. R. Brooks, D. Janežič and M. Karplus, Journal of Computational Chemistry, 16 (12) pp. 1522-1542 (1995). [DOI] [URL]

"Harmonic analysis of large systems. II. Comparison of different protein models," D. Janežič and B. R. Brooks, Journal of Computational Chemistry, 16 (12) pp. 1543-1553 (1995). [DOI] [URL]

"Harmonic analysis of large systems. III. Comparison with molecular dynamics," D. Janežič, R. M. Venable and B. R. Brooks, Journal of Computational Chemistry, 16 (12) pp. 1554-1566 (1995). [DOI] [URL]

1994

"Solvent-Induced Forces between Two Hydrophilic Groups," S. R. Durell, B. R. Brooks and A. Ben-Naim, The Journal of Physical Chemistry, 98 (8) pp. 2198-2202 (1994). [DOI] [URL]

"New spherical-cutoff methods for long-range forces in macromolecular simulation," P. J. Steinbach and B. R. Brooks, Journal of Computational Chemistry, 15 (7) pp. 667-683 (1994). [DOI] [URL]

1993

"Metabolism-based transformation of myoglobin to an oxidase by BrCCl3 and molecular modeling of the oxidase form," Y. Osawa, J. F. Darbyshire, P. J. Steinbach and B. R. Brooks, Journal of Biological Chemistry, 268 (4) pp. 2953-9 (1993). [URL]

"Theoretical studies of relaxation of a monomeric subunit of HIV-1 protease in water using molecular dynamics," R. M. Venable, F. W. Carson and B. R. Brooks, Proteins: Structure, Function, and Bioinformatics, 15 (4) pp. 374-384 (1993). [DOI] [URL]

"Protein hydration elucidated by molecular dynamics simulation," P. J. Steinbach and B. R. Brooks, Proceedings of the National Academy of Sciences, 90 (19) pp. 9135-9139 (1993). [URL]

1992

"Langevin dynamics of peptides: The frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide," R. J. Loncharich, B. R. Brooks and R. W. Pastor, Biopolymers, 32 (5) pp. 523-535 (1992). [DOI] [URL]

"A 500 ps molecular dynamics simulation study of interleukin-1β; in water," I. Chandrasekhar, G. Clore, A. Szabo, A. M. Gronenborn and B. R. Brooks, Journal of Molecular Biology, 226 (1) pp. 239 - 250 (1992). [DOI] [URL]

1990

"Molecular machanics and antibody binding in the structural analysis of polycyclic aromatic hydrocarbon-diol-epoxide-DNA adducts," A. Weston, M. J. Newman, D. L. Mann and B. R. Brooks, Carcinogenesis, 11 (5) pp. 859-864 (1990). [DOI] [URL]

"Solution conformations of the B-loop fragments of human transforming growth factor alpha and epidermal growth factor by 1H nuclear magnetic resonance and restrained molecular dynamics," K. H. Han, J. L. Syi, B. R. Brooks and J. A. Ferretti, Proceedings of the National Academy of Sciences, 87 (7) pp. 2818-2822 (1990). [URL]

"Temperature dependence of dynamics of hydrated myoglobin," R. J. Loncharich and B. R. Brooks, Journal of Molecular Biology, 215 (3) pp. 439 - 455 (1990). [DOI] [URL]

"Models of δ-hemolysin membrane channels and crystal structures," G. Raghunathan, P. Seetharamulu, B. R. Brooks and H. R. Guy, Proteins: Structure, Function, and Bioinformatics, 8 (3) pp. 213-225 (1990). [DOI] [URL]

1989

"The effects of truncating long-range forces on protein dynamics," R. J. Loncharich and B. R. Brooks, Proteins: Structure, Function, and Bioinformatics, 6 (1) pp. 32-45 (1989). [DOI] [URL]

1988

"An analysis of the accuracy of Langevin and molecular dynamics algorithms," R. W. Pastor, B. R. Brooks and A. Szabo, Molecular Physics, 65 (6) pp. 1409-1419 (1988). [DOI] [URL]

1987

"Theoretically determined three-dimensional structure for the repeating tetrapeptide unit of the circumsporozoite coat protein of the malaria parasite Plasmodium falciparum," B. R. Brooks, R. W. Pastor and F. W. Carson, Proceedings of the National Academy of Sciences, 84 (13) pp. 4470-4474 (1987). [URL]

1986

"Molecular dynamics simulations of native and substrate-bound lysozyme," C. B. Post, B. R. Brooks, M. Karplus, C. M. Dobson, P. J. Artymiuk, J. C. Cheetham and D. C. Phillips, Journal of Molecular Biology, 190 (3) pp. 455 - 479 (1986). [DOI] [URL]

1985

"Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme," B. Brooks and M. Karplus, Proceedings of the National Academy of Sciences, 82 (15) pp. 4995-4999 (1985). [URL]

"Transition from B to Z DNA: contribution of internal fluctuations to the configurational entropy difference," K. Irikura, B. Tidor, B. Brooks and M. Karplus, Science, 229 (4713) pp. 571-572 (1985). [DOI] [URL]

1983

"Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor," B. Brooks and M. Karplus, Proceedings of the National Academy of Sciences, 80 (21) pp. 6571-6575 (1983). [URL]

"Dynamics of DNA Oligomers," B. Tidor, K. K. Irikura, B. R. Brooks and M. Karplus, Journal of Biomolecular Structure and Dynamics, 1 (1) pp. 231-252 (1983). [DOI] [URL]

"CHARMM: A program for macromolecular energy, minimization, and dynamics calculations," B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan and M. Karplus, Journal of Computational Chemistry, 4 (2) pp. 187-217 (1983). [DOI] [URL]

1980

"Analytic gradients from correlated wave functions via the two-particle density matrix and the unitary group approach," B. R. Brooks, W. D. Laidig, P. Saxe, J. D. Goddard, Y. Yamaguchi and III Henry F. Schaefer, The Journal of Chemical Physics, 72 (8) pp. 4652-4653 (1980). [DOI] [URL]

1979

"Sudden polarization: pyramidalization of twisted ethylene," B. R. Brooks and H. F. Schaefer, Journal of the American Chemical Society, 101 (2) pp. 307-311 (1979). [DOI] [URL]

"Three isomers of the aluminum-acetylene system," M. Trenary, M. E. Casida, B. R. Brooks and H. F. Schaefer, Journal of the American Chemical Society, 101 (6) pp. 1638-1639 (1979). [DOI] [URL]

"The graphical unitary group approach to the electron correlation problem. Methods and preliminary applications," B. R. Brooks and III Henry F. Schaefer, The Journal of Chemical Physics, 70 (11) pp. 5092-5106 (1979). [DOI] [URL]