Ronald M. Levy
Orcid: 0000-0001-8696-5177
According to our database1,
Ronald M. Levy
authored at least 34 papers
between 1986 and 2022.
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Bibliography
2022
Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid.
J. Comput. Aided Mol. Des., 2022
2021
Mi3-GPU: MCMC-based inverse Ising inference on GPUs for protein covariation analysis.
Comput. Phys. Commun., 2021
2020
Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses.
J. Comput. Chem., 2020
2019
Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network.
J. Chem. Inf. Model., 2019
2018
Improving Prediction Accuracy of Binding Free Energies and Poses of HIV Integrase Complexes Using the Binding Energy Distribution Analysis Method with Flattening Potentials.
J. Chem. Inf. Model., 2018
2017
Computing conformational free energy differences in explicit solvent: An efficient thermodynamic cycle using an auxiliary potential and a free energy functional constructed from the end points.
J. Comput. Chem., 2017
Erratum to: A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge.
J. Comput. Aided Mol. Des., 2017
A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge.
J. Comput. Aided Mol. Des., 2017
2016
Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015.
J. Comput. Aided Mol. Des., 2016
2015
Deep Sequencing of Protease Inhibitor Resistant HIV Patient Isolates Reveals Patterns of Correlated Mutations in Gag and Protease.
PLoS Comput. Biol., 2015
Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis.
J. Comput. Chem., 2015
J. Comput. Aided Mol. Des., 2015
Comput. Phys. Commun., 2015
2014
Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge.
J. Comput. Aided Mol. Des., 2014
2013
Proceedings of the Extreme Science and Engineering Discovery Environment: Gateway to Discovery, 2013
2012
PLoS Comput. Biol., 2012
Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM).
J. Comput. Aided Mol. Des., 2012
2011
Identification of Alternative Binding Sites for Inhibitors of HIV-1 Ribonuclease H Through Comparative Analysis of Virtual Enrichment Studies.
J. Chem. Inf. Model., 2011
2010
Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting.
J. Comput. Chem., 2010
2009
Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease.
BMC Bioinform., 2009
2008
2007
Comparative Performance of Several Flexible Docking Programs and Scoring Functions: Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets.
J. Chem. Inf. Model., 2007
2006
Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular Dynamics Applications.
Proceedings of the 2006 International Conference on Parallel Processing (ICPP 2006), 2006
2005
J. Comput. Chem., 2005
2004
AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.
J. Comput. Chem., 2004
2003
Performance Management for Cluster Based Web Services.
Proceedings of the Integrated Network Management VII, Managing It All, 2003
2002
The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators.
J. Comput. Chem., 2002
2001
Solvent models for protein-ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations.
J. Comput. Chem., 2001
The Rutgers Computational Grid Based on Linux PC Cluster.
Proceedings of the Tenth SIAM Conference on Parallel Processing for Scientific Computing, 2001
2000
Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases.
Bioinform., 2000
1995
Evaluating Polarizable Potentials on Distributed Memory Parallel Computers: Program Development and Applications.
J. Comput. Chem., 1995
1986
Comput. Chem., 1986