Search Results - "Brooks, Bernard R." :: K.UTB vyhledávací portál | TBU Library Retrieval Portal

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

by Eastman, Peter, Swails, Jason, Chodera, John D, McGibbon, Robert T, Zhao, Yutong, Beauchamp, Kyle A, Wang, Lee-Ping, Simmonett, Andrew C, Harrigan, Matthew P, Stern, Chaya D, Wiewiora, Rafal P, Brooks, Bernard R, Pande, Vijay S
Published in PLoS computational biology (01.07.2017)

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Journal Article

Quantifying the effects of lossy compression on energies calculated from molecular dynamics trajectories

Quantifying the effects of lossy compression on energies calculated from molecular dynamics trajectories

by Roe, Daniel R., Brooks, Bernard R.
Published in Protein science (01.12.2022)

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A deep learning approach for the blind logP prediction in SAMPL6 challenge

A deep learning approach for the blind logP prediction in SAMPL6 challenge

by Prasad, Samarjeet, Brooks, Bernard R.
Published in Journal of computer-aided molecular design (01.05.2020)

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Conformational Fluctuations in β2-Microglubulin Using Markov State Modeling and Molecular Dynamics

Conformational Fluctuations in β2-Microglubulin Using Markov State Modeling and Molecular Dynamics

by Ghorbani, Mahdi, Brooks, Bernard R., Klauda, Jeffery B.
Published in The journal of physical chemistry. B (10.08.2023)

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The homogeneity condition: A simple way to derive isotropic periodic sum potentials for efficient calculation of long-range interactions in molecular simulation

The homogeneity condition: A simple way to derive isotropic periodic sum potentials for efficient calculation of long-range interactions in molecular simulation

by Wu, Xiongwu, Brooks, Bernard R
Published in The Journal of chemical physics (07.06.2019)

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Machine Learning Force Field Parameters from Ab Initio Data

Machine Learning Force Field Parameters from Ab Initio Data

by Li, Ying, Li, Hui, Pickard, Frank C, Narayanan, Badri, Sen, Fatih G, Chan, Maria K. Y, Sankaranarayanan, Subramanian K. R. S, Brooks, Bernard R, Roux, Benoît
Published in Journal of chemical theory and computation (12.09.2017)

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Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion

Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion

by Yu, Yalun, Krämer, Andreas, Venable, Richard M, Simmonett, Andrew C, MacKerell, Alexander D, Klauda, Jeffery B, Pastor, Richard W, Brooks, Bernard R
Published in Journal of chemical theory and computation (09.03.2021)

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pH replica-exchange method based on discrete protonation states

pH replica-exchange method based on discrete protonation states

by Itoh, Satoru G., Damjanović, Ana, Brooks, Bernard R.
Published in Proteins, structure, function, and bioinformatics (01.12.2011)

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Origin of pKa Shifts of Internal Lysine Residues in SNase Studied Via Equal-Molar VMMS Simulations in Explicit Water

Origin of pKa Shifts of Internal Lysine Residues in SNase Studied Via Equal-Molar VMMS Simulations in Explicit Water

by Wu, Xiongwu, Lee, Juyong, Brooks, Bernard R
Published in The journal of physical chemistry. B (20.04.2017)

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Mapping the Drude polarizable force field onto a multipole and induced dipole model

Mapping the Drude polarizable force field onto a multipole and induced dipole model

by Huang, Jing, Simmonett, Andrew C, Pickard, 4th, Frank C, MacKerell, Jr, Alexander D, Brooks, Bernard R
Published in The Journal of chemical physics (28.10.2017)

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Finding multiple reaction pathways via global optimization of action

Finding multiple reaction pathways via global optimization of action

by Lee, Juyong, Lee, In-Ho, Joung, InSuk, Lee, Jooyoung, Brooks, Bernard R.
Published in Nature communications (26.05.2017)

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Journal Article

A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water

A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water

by Wu, Xiongwu, Brooks, Bernard R
Published in PLoS computational biology (01.10.2015)

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Absolute and relative pKa predictions via a DFT approach applied to the SAMPL6 blind challenge

Absolute and relative pKa predictions via a DFT approach applied to the SAMPL6 blind challenge

by Zeng, Qiao, Jones, Michael R., Brooks, Bernard R.
Published in Journal of computer-aided molecular design (01.10.2018)

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Low-Frequency Normal Modes That Describe Allosteric Transitions in Biological Nanomachines Are Robust to Sequence Variations

Low-Frequency Normal Modes That Describe Allosteric Transitions in Biological Nanomachines Are Robust to Sequence Variations

by Zheng, Wenjun, Brooks, Bernard R., Thirumalai, D.
Published in Proceedings of the National Academy of Sciences - PNAS (16.05.2006)

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Protein conformational transitions explored by mixed elastic network models

Protein conformational transitions explored by mixed elastic network models

by Zheng, Wenjun, Brooks, Bernard R., Hummer, Gerhard
Published in Proteins, structure, function, and bioinformatics (01.10.2007)

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A double exponential potential for van der Waals interaction

A double exponential potential for van der Waals interaction

by Wu, Xiongwu, Brooks, Bernard R.
Published in AIP advances (01.06.2019)

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A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes

A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes

by König, Gerhard, Pickard, Frank C, Huang, Jing, Thiel, Walter, MacKerell, Alexander D, Brooks, Bernard R, York, Darrin M
Published in Molecules (Basel, Switzerland) (19.10.2018)

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Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model

Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model

by O'Brien, Edward P, Ziv, Guy, Haran, Gilad, Brooks, Bernard R, Thirumalai, D
Published in Proceedings of the National Academy of Sciences - PNAS (09.09.2008)

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Interactions of Water and Alkanes: Modifying Additive Force Fields to Account for Polarization Effects

Interactions of Water and Alkanes: Modifying Additive Force Fields to Account for Polarization Effects

by Krämer, Andreas, Pickard, Frank C, Huang, Jing, Venable, Richard M, Simmonett, Andrew C, Reith, Dirk, Kirschner, Karl N, Pastor, Richard W, Brooks, Bernard R
Published in Journal of chemical theory and computation (11.06.2019)

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Isotropic periodic sum for multipole interactions and a vector relation for calculation of the Cartesian multipole tensor

Isotropic periodic sum for multipole interactions and a vector relation for calculation of the Cartesian multipole tensor

by Wu, Xiongwu, Pickard, 4th, Frank C, Brooks, Bernard R
Published in The Journal of chemical physics (28.10.2016)

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