Ronald M. Levy
According to our database1, Ronald M. Levy authored at least 33 papers between 1986 and 2021.
Legend:Book In proceedings Article PhD thesis Other
Mi3-GPU: MCMC-based inverse Ising inference on GPUs for protein covariation analysis.
Comput. Phys. Commun., 2021
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
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
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
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
Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015.
J. Comput. Aided Mol. Des., 2016
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
Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge.
J. Comput. Aided Mol. Des., 2014
Proceedings of the Extreme Science and Engineering Discovery Environment: Gateway to Discovery, 2013
PLoS Comput. Biol., 2012
Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM).
J. Comput. Aided Mol. Des., 2012
Identification of Alternative Binding Sites for Inhibitors of HIV-1 Ribonuclease H Through Comparative Analysis of Virtual Enrichment Studies.
J. Chem. Inf. Model., 2011
Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting.
J. Comput. Chem., 2010
Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease.
BMC Bioinform., 2009
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
Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular Dynamics Applications.
Proceedings of the 2006 International Conference on Parallel Processing (ICPP 2006), 2006
J. Comput. Chem., 2005
AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.
J. Comput. Chem., 2004
Performance Management for Cluster Based Web Services.
Proceedings of the Integrated Network Management VII, Managing It All, 2003
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
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
Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases.
Evaluating Polarizable Potentials on Distributed Memory Parallel Computers: Program Development and Applications.
J. Comput. Chem., 1995
Comput. Chem., 1986