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2020 – today
- 2024
[j46]Daniel R. Roe
, Bernard R. Brooks:
MPI-parallelization of the grid inhomogeneous solvation theory calculation. J. Comput. Chem. 45(10): 633-637 (2024)- 2022
- [j45]Phillip S. Hudson, Félix Aviat, Rubén Meana-Pañeda, Luke C. Warrensford, Benjamin C. Pollard, Samarjeet Prasad, Michael R. Jones, H. Lee Woodcock III, Bernard R. Brooks:
Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches. J. Comput. Aided Mol. Des. 36(4): 263-277 (2022) - [i3]Mahdi Ghorbani, Samarjeet Prasad, Jeffery B. Klauda, Bernard R. Brooks:
GraphVAMPNet, using graph neural networks and variational approach to markov processes for dynamical modeling of biomolecules. CoRR abs/2201.04609 (2022) - 2021
- [j44]Mahdi Ghorbani, Phillip S. Hudson, Michael R. Jones, Félix Aviat, Rubén Meana-Pañeda, Jeffery B. Klauda, Bernard R. Brooks:
A replica exchange umbrella sampling (REUS) approach to predict host-guest binding free energies in SAMPL8 challenge. J. Comput. Aided Mol. Des. 35(5): 667-677 (2021) - [j43]Samarjeet Prasad, Andrew C. Simmonett, Rubén Meana-Pañeda, Bernard R. Brooks:
The Extended Eighth-Shell method for periodic boundary conditions with rotational symmetry. J. Comput. Chem. 42(19): 1373-1383 (2021) - [i2]Mahdi Ghorbani, Samarjeet Prasad, Jeffery B. Klauda, Bernard R. Brooks:
Variational embedding of protein folding simulations using gaussian mixture variational autoencoders. CoRR abs/2108.12493 (2021) - 2020
- [j42]Andreas Krämer, Phillip S. Hudson, Michael R. Jones, Bernard R. Brooks:
Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water-octanol partition coefficients in the SAMPL6 challenge. J. Comput. Aided Mol. Des. 34(5): 471-483 (2020) - [j41]Michael R. Jones, Bernard R. Brooks:
Quantum chemical predictions of water-octanol partition coefficients applied to the SAMPL6 logP blind challenge. J. Comput. Aided Mol. Des. 34(5): 485-493 (2020) - [j40]Prajay Patel, David M. Kuntz, Michael R. Jones, Bernard R. Brooks, Angela K. Wilson:
SAMPL6 logP challenge: machine learning and quantum mechanical approaches. J. Comput. Aided Mol. Des. 34(5): 495-510 (2020) - [j39]Samarjeet Prasad, Bernard R. Brooks:
A deep learning approach for the blind logP prediction in SAMPL6 challenge. J. Comput. Aided Mol. Des. 34(5): 535-542 (2020)
2010 – 2019
- 2018
- [j38]Phillip S. Hudson, Kyungreem Han, H. Lee Woodcock III, Bernard R. Brooks:
Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale. J. Comput. Aided Mol. Des. 32(10): 983-999 (2018) - [j37]Kyungreem Han, Phillip S. Hudson, Michael R. Jones, Naohiro Nishikawa, Florentina Tofoleanu, Bernard R. Brooks:
Prediction of CB[8] host-guest binding free energies in SAMPL6 using the double-decoupling method. J. Comput. Aided Mol. Des. 32(10): 1059-1073 (2018) - [j36]Naohiro Nishikawa, Kyungreem Han, Xiongwu Wu, Florentina Tofoleanu, Bernard R. Brooks:
Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges. J. Comput. Aided Mol. Des. 32(10): 1075-1086 (2018) - [j35]Qiao Zeng, Michael R. Jones, Bernard R. Brooks:
Absolute and relative pK a predictions via a DFT approach applied to the SAMPL6 blind challenge. J. Comput. Aided Mol. Des. 32(10): 1179-1189 (2018) - [j34]Samarjeet Prasad, Jing Huang, Qiao Zeng, Bernard R. Brooks:
An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge. J. Comput. Aided Mol. Des. 32(10): 1191-1201 (2018) - 2017
- [j33]Juyong Lee, Florentina Tofoleanu, Frank C. Pickard IV, Gerhard König, Jing Huang, Ana Damjanovic, Minkyung Baek, Chaok Seok, Bernard R. Brooks:
Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge. J. Comput. Aided Mol. Des. 31(1): 71-85 (2017) - [j32]Florentina Tofoleanu, Juyong Lee, Frank C. Pickard IV, Gerhard König, Jing Huang, Minkyung Baek, Chaok Seok, Bernard R. Brooks:
Absolute binding free energies for octa-acids and guests in SAMPL5 - Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge. J. Comput. Aided Mol. Des. 31(1): 107-118 (2017) - [j31]Meiting Wang, Pengfei Li, Xiangyu Jia, Wei Liu, Yihan Shao, Wenxin Hu, Jun Zheng, Bernard R. Brooks, Ye Mei:
Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level. J. Chem. Inf. Model. 57(10): 2476-2489 (2017) - [j30]Peter K. Eastman, Jason M. Swails, John D. Chodera, Robert McGibbon, Yutong Zhao, Kyle Beauchamp, Lee-Ping Wang, Andrew C. Simmonett, Matthew P. Harrigan, Chaya D. Stern, Rafal P. Wiewiora, Bernard R. Brooks, Vijay S. Pande:
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLoS Comput. Biol. 13(7) (2017) - 2016
- [j29]Gerhard König, Frank C. Pickard IV, Jing Huang, Andrew C. Simmonett, Florentina Tofoleanu, Juyong Lee, Pavlo O. Dral, Samarjeet Prasad, Michael R. Jones, Yihan Shao, Walter Thiel, Bernard R. Brooks:
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. J. Comput. Aided Mol. Des. 30(11): 989-1006 (2016) - [j28]Frank C. Pickard IV, Gerhard König, Florentina Tofoleanu, Juyong Lee, Andrew C. Simmonett, Yihan Shao, Jay W. Ponder, Bernard R. Brooks:
Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections. J. Comput. Aided Mol. Des. 30(11): 1087-1100 (2016) - [j27]Michael R. Jones, Bernard R. Brooks, Angela K. Wilson:
Partition coefficients for the SAMPL5 challenge using transfer free energies. J. Comput. Aided Mol. Des. 30(11): 1129-1138 (2016) - [j26]Xiongwu Wu, Bernard R. Brooks, Eric Vanden-Eijnden:
Self-guided Langevin dynamics via generalized Langevin equation. J. Comput. Chem. 37(6): 595-601 (2016) - [i1]Juyong Lee, Zhong-Yuan Zhang, Jooyoung Lee, Bernard R. Brooks, Yong-Yeol Ahn:
Link community detection through global optimization and the inverse resolution limit of partition density. CoRR abs/1601.05100 (2016) - 2015
- [j25]Juyong Lee, Kiho Lee, InSuk Joung, Keehyoung Joo, Bernard R. Brooks, Jooyoung Lee:
Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest. BMC Bioinform. 16: 94:1-94:12 (2015) - [j24]Iwona E. Weidlich, Yuri Pevzner, Benjamin T. Miller, Igor V. Filippov, H. Lee Woodcock III, Bernard R. Brooks:
Development and implementation of (Q)SAR modeling within the CHARMMing web-user interface. J. Comput. Chem. 36(1): 62-67 (2015) - [j23]Janez Konc, Benjamin T. Miller, Tanja Stular, Samo Lesnik, H. Lee Woodcock III, Bernard R. Brooks, Dusanka Janezic:
ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites. J. Chem. Inf. Model. 55(11): 2308-2314 (2015) - [j22]Xiongwu Wu, Bernard R. Brooks:
A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water. PLoS Comput. Biol. 11(10) (2015) - 2014
- [j21]Gerhard König, Frank C. Pickard IV, Ye Mei, Bernard R. Brooks:
Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4. J. Comput. Aided Mol. Des. 28(3): 245-257 (2014) - [j20]Benjamin T. Miller, Rishi P. Singh, Vinushka Schalk, Yuri Pevzner, Jingjun Sun, Carrie S. Miller, Stefan Boresch, Toshiko Ichiye, Bernard R. Brooks, H. Lee Woodcock III:
Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial. PLoS Comput. Biol. 10(7) (2014) - [j19]Bradley Scott Perrin Jr., Benjamin T. Miller, Vinushka Schalk, H. Lee Woodcock III, Bernard R. Brooks, Toshiko Ichiye:
Web-Based Computational Chemistry Education with CHARMMing III: Reduction Potentials of Electron Transfer Proteins. PLoS Comput. Biol. 10(7) (2014) - [j18]Frank C. Pickard IV, Benjamin T. Miller, Vinushka Schalk, Michael G. Lerner, H. Lee Woodcock III, Bernard R. Brooks:
Web-Based Computational Chemistry Education with CHARMMing II: Coarse-Grained Protein Folding. PLoS Comput. Biol. 10(7) (2014) - 2012
- [j17]Gerhard König, Bernard R. Brooks:
Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations. J. Comput. Aided Mol. Des. 26(5): 543-550 (2012) - [j16]Pradip K. Biswas, Nadeem A. Vellore, Jeremy A. Yancey, Tugba G. Kucukkal, Galen Collier, Bernard R. Brooks, Steven J. Stuart, Robert A. Latour:
Simulation of multiphase systems utilizing independent force fields to control intraphase and interphase behavior. J. Comput. Chem. 33(16): 1458-1466 (2012) - [j15]An Ghysels, Benjamin T. Miller, Frank C. Pickard IV, Bernard R. Brooks:
Comparing normal modes across different models and scales: Hessian reduction versus coarse-graining. J. Comput. Chem. 33(28): 2250-2275 (2012) - [j14]Nejc Carl, Milan Hodoscek, Blaz Vehar, Janez Konc, Bernard R. Brooks, Dusanka Janezic:
Correlating Protein Hot Spot Surface Analysis Using ProBiS with Simulated Free Energies of Protein-Protein Interfacial Residues. J. Chem. Inf. Model. 52(10): 2541-2549 (2012) - 2011
- [j13]Urban Borstnik, Benjamin T. Miller, Bernard R. Brooks, Dusanka Janezic:
The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations. J. Comput. Chem. 32(14): 3005-3013 (2011) - 2010
- [j12]An Ghysels, Veronique Van Speybroeck, Ewald Pauwels, Saron Catak, Bernard R. Brooks, Dimitri Van Neck, Michel Waroquier:
Comparative study of various normal mode analysis techniques based on partial Hessians. J. Comput. Chem. 31(5): 994-1007 (2010)
2000 – 2009
- 2009
- [j11]Bernard R. Brooks, Charles L. Brooks III, Alexander D. MacKerell Jr., Lennart Nilsson, Robert J. Petrella, Benoît Roux, Y. Won, G. Archontis, Christian Bartels, Stefan Boresch, Amedeo Caflisch, Leo S. D. Caves, Qiang Cui, Aaron R. Dinner, Michael Feig, S. Fischer, Jiali Gao, Milan Hodoscek, Wonpil Im, Krzysztof Kuczera, Themis Lazaridis, J. Ma, Victor Ovchinnikov, Emanuele Paci, Richard W. Pastor, C. B. Post, J. Z. Pu, Michael Schaefer, Bruce Tidor, Richard M. Venable, H. Lee Woodcock III, X. Wu, W. Yang, Darrin M. York, Martin Karplus:
CHARMM: The biomolecular simulation program. J. Comput. Chem. 30(10): 1545-1614 (2009) - [j10]Edina Rosta, H. Lee Woodcock III, Bernard R. Brooks, Gerhard Hummer:
Artificial reaction coordinate "tunneling" in free-energy calculations: The catalytic reaction of RNase H. J. Comput. Chem. 30(11): 1634-1641 (2009) - 2008
- [j9]Benjamin T. Miller, Rishi P. Singh, Jeffery B. Klauda, Milan Hodoscek, Bernard R. Brooks, H. Lee Woodcock III:
CHARMMing: A New, Flexible Web Portal for CHARMM. J. Chem. Inf. Model. 48(9): 1920-1929 (2008) - [j8]Ana Damjanovic, Benjamin T. Miller, Torre J. Wenaus, Petar Maksimovic, Bertrand García-Moreno E., Bernard R. Brooks:
Open Science Grid Study of the Coupling between Conformation and Water Content in the Interior of a Protein. J. Chem. Inf. Model. 48(10): 2021-2029 (2008) - 2007
- [j7]H. Lee Woodcock III, Milan Hodoscek, Andrew T. B. Gilbert, Peter M. W. Gill, Henry F. Schaefer III, Bernard R. Brooks:
Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations. J. Comput. Chem. 28(9): 1485-1502 (2007) - [c1]Xiongwu Wu, Bernard R. Brooks:
Modeling Of Macromolecular Assemblies with Map Objects. BIOCOMP 2007: 411-420 - 2006
- [j6]Ye Che, Bernard R. Brooks, Garland R. Marshall:
Development of small molecules designed to modulate protein-protein interactions. J. Comput. Aided Mol. Des. 20(2): 109-130 (2006) - 2004
- [j5]Xiongwu Wu, Yidong Chen, Bernard R. Brooks, Yan A. Su:
The Local Maximum Clustering Method and Its Application in Microarray Gene Expression Data Analysis. EURASIP J. Adv. Signal Process. 2004(1): 53-63 (2004) - 2003
- [j4]Robert J. Petrella, Ioan Andricioaei, Bernard R. Brooks, Martin Karplus:
An improved method for nonbonded list generation: Rapid determination of near-neighbor pairs. J. Comput. Chem. 24(2): 222-231 (2003)
1990 – 1999
- 1995
- [j3]Bernard R. Brooks, Dusanka Janezic, Martin Karplus:
Harmonic Analysis of Large Systems. I. Methodology. J. Comput. Chem. 16(12): 1522-1542 (1995) - 1994
- [j2]Philippe Derreumaux, Guihua Zhang, Tamar Schlick, Bernard R. Brooks:
A Truncated Newton Minimizer Adapted for CHARMM and Biomolecular Applications. J. Comput. Chem. 15(5): 532-552 (1994) - [j1]Peter J. Steinbach, Bernard R. Brooks:
New Spherical-Cutoff Methods for Long-Range Forces in Macromolecular Simulation. J. Comput. Chem. 15(7): 667-683 (1994)
Coauthor Index
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