Ronald M. Levy

Publication Activity (10 Years)

Years Active: 1986-2022
Publications (10 Years): 10

Top Topics

Virtual Screening

Belief Propagation

Top Venues

J. Comput. Aided Mol. Des.

J. Comput. Chem.

Comput. Phys. Commun.

J. Chem. Inf. Model.

Publications

Qinfang Sun, Avik Biswas, R. S. K. Vijayan, Pierrick Craveur, Stefano Forli, Arthur J. Olson, Andres Emanuelli Castaner, Karen Kirby, Stefan G. Sarafianos, Nan-Jie Deng, Ronald M. Levy
Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid. J. Comput. Aided Mol. Des. 36 (3) (2022)
Allan Haldane, Ronald M. Levy
Mi3-GPU: MCMC-based inverse Ising inference on GPUs for protein covariation analysis. Comput. Phys. Commun. 260 (2021)
Francisco McGee, Quentin Novinger, Ronald M. Levy, Vincenzo Carnevale, Allan Haldane
Generative Capacity of Probabilistic Protein Sequence Models. CoRR (2020)
Yoshitake Sakae, Bin W. Zhang, Ronald M. Levy, Nan-Jie Deng
Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses. J. Comput. Chem. 41 (1) (2020)
Junchao Xia, William F. Flynn, Emilio Gallicchio, Keith Uplinger, Jonathan D. Armstrong, Stefano Forli, Arthur J. Olson, Ronald M. Levy
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. 59 (4) (2019)
Junchao Xia, William F. Flynn, Ronald M. Levy
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. 58 (7) (2018)
Rajat Kumar Pal, Kamran Haider, Divya Kaur, William F. Flynn, Junchao Xia, Ronald M. Levy, Tetiana Taran, Lauren Wickstrom, Tom Kurtzman, Emilio Gallicchio
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. 31 (1) (2017)
Robert C. Harris, Nan-Jie Deng, Ronald M. Levy, Ryosuke Ishizuka, Nobuyuki Matubayasi
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. 38 (15) (2017)
Rajat Kumar Pal, Kamran Haider, Divya Kaur, William F. Flynn, Junchao Xia, Ronald M. Levy, Tetiana Taran, Lauren Wickstrom, Tom Kurtzman, Emilio Gallicchio
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. 31 (1) (2017)
Nan-Jie Deng, William F. Flynn, Junchao Xia, R. S. K. Vijayan, Baofeng Zhang, Peng He, Ahmet Mentes, Emilio Gallicchio, Ronald M. Levy
Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015. J. Comput. Aided Mol. Des. 30 (9) (2016)
William F. Flynn, Max W. Chang, Zhiqiang Tan, Glenn Oliveira, Jinyun Yuan, Jason F. Okulicz, Bruce E. Torbett, Ronald M. Levy
Deep Sequencing of Protease Inhibitor Resistant HIV Patient Isolates Reveals Patterns of Correlated Mutations in Gag and Protease. PLoS Comput. Biol. 11 (4) (2015)
Junchao Xia, William F. Flynn, Emilio Gallicchio, Bin W. Zhang, Peng He, Zhiqiang Tan, Ronald M. Levy
Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis. J. Comput. Chem. 36 (23) (2015)
Emilio Gallicchio, Junchao Xia, William F. Flynn, Baofeng Zhang, Sade Samlalsingh, Ahmet Mentes, Ronald M. Levy
Asynchronous replica exchange software for grid and heterogeneous computing. Comput. Phys. Commun. 196 (2015)
Emilio Gallicchio, Haoyuan Chen, He Chen, Michael Fitzgerald, Yang Gao, Peng He, Malathi Kalyanikar, Chuan Kao, Beidi Lu, Yijie Niu, Manasi A. Pethe, Jie Zhu, Ronald M. Levy
BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge. J. Comput. Aided Mol. Des. 29 (4) (2015)
Emilio Gallicchio, Nan-Jie Deng, Peng He, Lauren Wickstrom, Alexander L. Perryman, Daniel N. Santiago, Stefano Forli, Arthur J. Olson, Ronald M. Levy
Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge. J. Comput. Aided Mol. Des. 28 (4) (2014)
Brian K. Radak, Tai-Sung Lee, Peng He, Melissa Romanus, Ole Weidner, Wei Dai, Emilio Gallicchio, Nan-Jie Deng, Darrin M. York, Ronald M. Levy, Shantenu Jha
A framework for flexible and scalable replica-exchange on production distributed CI. XSEDE (2013)
Omar Haq, Michael Andrec, Alexandre V. Morozov, Ronald M. Levy
Correlated Electrostatic Mutations Provide a Reservoir of Stability in HIV Protease. PLoS Comput. Biol. 8 (9) (2012)
Emilio Gallicchio, Ronald M. Levy
Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM). J. Comput. Aided Mol. Des. 26 (5) (2012)
Anthony K. Felts, Krystal LaBarge, Joseph D. Bauman, Dishaben V. Patel, Daniel Himmel, Eddy Arnold, Michael A. Parniak, Ronald M. Levy
Identification of Alternative Binding Sites for Inhibitors of HIV-1 Ribonuclease H Through Comparative Analysis of Virtual Enrichment Studies. J. Chem. Inf. Model. 51 (8) (2011)
Hisashi Okumura, Emilio Gallicchio, Ronald M. Levy
Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting. J. Comput. Chem. 31 (7) (2010)
Omar Haq, Ronald M. Levy, Alexandre V. Morozov, Michael Andrec
Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease. BMC Bioinform. 10 (S-8) (2009)
Emilio Gallicchio, Ronald M. Levy, Manish Parashar
Asynchronous replica exchange for molecular simulations. J. Comput. Chem. 29 (5) (2008)
Zhiyong Zhou, Anthony K. Felts, Richard A. Friesner, Ronald M. Levy
Comparative Performance of Several Flexible Docking Programs and Scoring Functions: Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets. J. Chem. Inf. Model. 47 (4) (2007)
Li Zhang, Manish Parashar, Emilio Gallicchio, Ronald M. Levy
Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular Dynamics Applications. ICPP (2006)
Jay L. Banks, Hege S. Beard, Yixiang X. Cao, Art E. Cho, Wolfgang Damm, Ramy Farid, Anthony K. Felts, Thomas A. Halgren, Daniel T. Mainz, Jon R. Maple, Robert B. Murphy, Dean M. Philipp, Matthew P. Repasky, Linda Yu Zhang, Bruce J. Berne, Richard A. Friesner, Emilio Gallicchio, Ronald M. Levy
Integrated Modeling Program, Applied Chemical Theory (IMPACT). J. Comput. Chem. 26 (16) (2005)
Emilio Gallicchio, Ronald M. Levy
AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. J. Comput. Chem. 25 (4) (2004)
Boris M. Chernyavsky, Emilio Gallicchio, Doyle D. Knight, Ronald M. Levy, Andy Page
The Rutgers Computational Grid: A Distributed Linux PC Cluster. Clust. Comput. 6 (3) (2003)
Ronald M. Levy, Jay Nagarajarao, Giovanni Pacifici, Mike Spreitzer, Asser N. Tantawi, Alaa Youssef
Performance Management for Cluster Based Web Services. Integrated Network Management (2003)
Emilio Gallicchio, Linda Yu Zhang, Ronald M. Levy
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. 23 (5) (2002)
Linda Yu Zhang, Emilio Gallicchio, Richard A. Friesner, Ronald M. Levy
Solvent models for protein-ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations. J. Comput. Chem. 22 (6) (2001)
Boris M. Chernyavsky, Emilio Gallicchio, Doyle D. Knight, Ronald M. Levy
The Rutgers Computational Grid Based on Linux PC Cluster. PPSC (2001)
Anders Wallqvist, Yoshifumi Fukunishi, Lynne Reed Murphy, Addi Fadel, Ronald M. Levy
Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases. Bioinform. 16 (11) (2000)
Dan N. Bernardo, Yanbo Ding, Karsten Krogh-Jespersen, Ronald M. Levy
Evaluating Polarizable Potentials on Distributed Memory Parallel Computers: Program Development and Applications. J. Comput. Chem. 16 (9) (1995)
Steven L. Gallion, Ronald M. Levy, Paul K. Weiner, Fumio Hirata
Implementation of a macromolecular mechanics program on a cyber 205 supercomputer. Comput. Chem. 10 (3) (1986)