Bernard R. Brooks
Orcid: 0000-0002-3586-2730
According to our database1,
Bernard R. Brooks
authored at least 50 papers
between 1994 and 2024.
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Bibliography
2024
J. Comput. Chem., April, 2024
2022
Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches.
J. Comput. Aided Mol. Des., 2022
GraphVAMPNet, using graph neural networks and variational approach to markov processes for dynamical modeling of biomolecules.
CoRR, 2022
2021
The Extended Eighth-Shell method for periodic boundary conditions with rotational symmetry.
J. Comput. Chem., 2021
A replica exchange umbrella sampling (REUS) approach to predict host-guest binding free energies in SAMPL8 challenge.
J. Comput. Aided Mol. Des., 2021
Variational embedding of protein folding simulations using gaussian mixture variational autoencoders.
CoRR, 2021
2020
J. Comput. Aided Mol. Des., 2020
J. Comput. Aided Mol. Des., 2020
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., 2020
Quantum chemical predictions of water-octanol partition coefficients applied to the SAMPL6 logP blind challenge.
J. Comput. Aided Mol. Des., 2020
2018
Absolute and relative pK a predictions via a DFT approach applied to the SAMPL6 blind challenge.
J. Comput. Aided Mol. Des., 2018
An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge.
J. Comput. Aided Mol. Des., 2018
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., 2018
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., 2018
Prediction of CB[8] host-guest binding free energies in SAMPL6 using the double-decoupling method.
J. Comput. Aided Mol. Des., 2018
2017
Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level.
J. Chem. Inf. Model., October, 2017
PLoS Comput. Biol., 2017
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., 2017
Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge.
J. Comput. Aided Mol. Des., 2017
2016
J. Comput. Chem., 2016
Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and p<i>K</i> <sub>a</sub> corrections.
J. Comput. Aided Mol. Des., 2016
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., 2016
J. Comput. Aided Mol. Des., 2016
Link community detection through global optimization and the inverse resolution limit of partition density.
CoRR, 2016
2015
A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water.
PLoS Comput. Biol., 2015
ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites.
J. Chem. Inf. Model., 2015
Development and implementation of (Q)SAR modeling within the CHARMMing web-user interface.
J. Comput. Chem., 2015
Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest.
BMC Bioinform., 2015
2014
Web-Based Computational Chemistry Education with CHARMMing II: Coarse-Grained Protein Folding.
PLoS Comput. Biol., 2014
Web-Based Computational Chemistry Education with CHARMMing III: Reduction Potentials of Electron Transfer Proteins.
PLoS Comput. Biol., 2014
PLoS Comput. Biol., 2014
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., 2014
2012
Correlating Protein Hot Spot Surface Analysis Using ProBiS with Simulated Free Energies of Protein-Protein Interfacial Residues.
J. Chem. Inf. Model., 2012
Comparing normal modes across different models and scales: Hessian reduction <i>versus</i> coarse-graining.
J. Comput. Chem., 2012
Simulation of multiphase systems utilizing independent force fields to control intraphase and interphase behavior.
J. Comput. Chem., 2012
Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations.
J. Comput. Aided Mol. Des., 2012
2011
The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations.
J. Comput. Chem., 2011
2010
Comparative study of various normal mode analysis techniques based on partial Hessians.
J. Comput. Chem., 2010
2009
Artificial reaction coordinate "tunneling" in free-energy calculations: The catalytic reaction of RNase H.
J. Comput. Chem., 2009
2008
Open Science Grid Study of the Coupling between Conformation and Water Content in the Interior of a Protein.
J. Chem. Inf. Model., 2008
2007
J. Comput. Chem., 2007
Modeling Of Macromolecular Assemblies with Map Objects.
Proceedings of the International Conference on Bioinformatics & Computational Biology, 2007
2006
J. Comput. Aided Mol. Des., 2006
2004
The Local Maximum Clustering Method and Its Application in Microarray Gene Expression Data Analysis.
EURASIP J. Adv. Signal Process., 2004
2003
An improved method for nonbonded list generation: Rapid determination of near-neighbor pairs.
J. Comput. Chem., 2003
1995
1994
J. Comput. Chem., 1994
J. Comput. Chem., 1994