Ronald M. Levy

According to our database1, Ronald M. Levy authored at least 33 papers between 1986 and 2021.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

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PhD thesis 
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Bibliography

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

Generative Capacity of Probabilistic Protein Sequence Models.
CoRR, 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

BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge.
J. Comput. Aided Mol. Des., 2015

Asynchronous replica exchange software for grid and heterogeneous computing.
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
A framework for flexible and scalable replica-exchange on production distributed CI.
Proceedings of the Extreme Science and Engineering Discovery Environment: Gateway to Discovery, 2013

2012
Correlated Electrostatic Mutations Provide a Reservoir of Stability in HIV Protease.
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
Asynchronous replica exchange for molecular simulations.
J. Comput. Chem., 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
Integrated Modeling Program, Applied Chemical Theory (IMPACT).
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
The Rutgers Computational Grid: A Distributed Linux PC Cluster.
Clust. Comput., 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
Implementation of a macromolecular mechanics program on a cyber 205 supercomputer.
Comput. Chem., 1986


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