Implementation of a macromolecular mechanics program on a cyber 205 supercomputer. - Steven L. Gallion; Ronald M. Levy; Paul K. Weiner; Fumio Hirata (Comput. Chem., 1986)

Evaluating Polarizable Potentials on Distributed Memory Parallel Computers: Program Development and Applications. - Dan N. Bernardo; Yanbo Ding; Karsten Krogh-Jespersen; Ronald M. Levy (J. Comput. Chem., 1995)

Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases. - Anders Wallqvist; Yoshifumi Fukunishi; Lynne Reed Murphy; Addi Fadel; Ronald M. Levy (Bioinform., 2000)

The Rutgers Computational Grid Based on Linux PC Cluster. - Boris M. Chernyavsky; Emilio Gallicchio; Doyle D. Knight; Ronald M. Levy (PP, 2001)

Solvent models for protein-ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations. - Linda Yu Zhang; Emilio Gallicchio; Richard A. Friesner; Ronald M. Levy (J. Comput. Chem., 2001)

The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators. - Emilio Gallicchio; Linda Yu Zhang; Ronald M. Levy (J. Comput. Chem., 2002)

Performance Management for Cluster Based Web Services. - Ronald M. Levy; Jay Nagarajarao; Giovanni Pacifici; Mike Spreitzer; Asser N. Tantawi; Alaa Youssef (Integrated Network Management, 2003)

The Rutgers Computational Grid: A Distributed Linux PC Cluster. - Boris M. Chernyavsky; Emilio Gallicchio; Doyle D. Knight; Ronald M. Levy; Andy Page (Clust. Comput., 2003)

AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. - Emilio Gallicchio; Ronald M. Levy (J. Comput. Chem., 2004)

Integrated Modeling Program, Applied Chemical Theory (IMPACT). - 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; et al. (J. Comput. Chem., 2005)

Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular Dynamics Applications. - Li Zhang; Manish Parashar; Emilio Gallicchio; Ronald M. Levy (ICPP, 2006)

Comparative Performance of Several Flexible Docking Programs and Scoring Functions: Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets. - Zhiyong Zhou; Anthony K. Felts; Richard A. Friesner; Ronald M. Levy (J. Chem. Inf. Model., 2007)

Asynchronous replica exchange for molecular simulations. - Emilio Gallicchio; Ronald M. Levy; Manish Parashar (J. Comput. Chem., 2008)

Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease. - Omar Haq; Ronald M. Levy; Alexandre V. Morozov; Michael Andrec (BMC Bioinform., 2009)

Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting. - Hisashi Okumura; Emilio Gallicchio; Ronald M. Levy (J. Comput. Chem., 2010)

Identification of Alternative Binding Sites for Inhibitors of HIV-1 Ribonuclease H Through Comparative Analysis of Virtual Enrichment Studies. - Anthony K. Felts; Krystal LaBarge; Joseph D. Bauman; Dishaben V. Patel; Daniel Himmel; Eddy Arnold; Michael A. Parniak; Ronald M. Levy (J. Chem. Inf. Model., 2011)

Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM). - Emilio Gallicchio; Ronald M. Levy (J. Comput. Aided Mol. Des., 2012)

Correlated Electrostatic Mutations Provide a Reservoir of Stability in HIV Protease. - Omar Haq; Michael Andrec; Alexandre V. Morozov; Ronald M. Levy (PLoS Comput. Biol., 2012)

A framework for flexible and scalable replica-exchange on production distributed CI. - 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 (XSEDE, 2013)

Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge. - Emilio Gallicchio; Nan-Jie Deng; Peng He; Lauren Wickstrom; Alexander L. Perryman; Daniel N. Santiago; Stefano Forli; Arthur J. Olson; Ronald M. Levy (J. Comput. Aided Mol. Des., 2014)

Asynchronous replica exchange software for grid and heterogeneous computing. - Emilio Gallicchio; Junchao Xia; William F. Flynn; Baofeng Zhang; Sade Samlalsingh; Ahmet Mentes; Ronald M. Levy (Comput. Phys. Commun., 2015)

BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge. - Emilio Gallicchio; Haoyuan Chen; He Chen; Michael Fitzgerald; Yang Gao 019; Peng He; Malathi Kalyanikar; Chuan Kao; Beidi Lu; Yijie Niu; Manasi A. Pethe; Jie Zhu; et al. (J. Comput. Aided Mol. Des., 2015)

Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis. - Junchao Xia; William F. Flynn; Emilio Gallicchio; Bin W. Zhang; Peng He; Zhiqiang Tan; Ronald M. Levy (J. Comput. Chem., 2015)

Deep Sequencing of Protease Inhibitor Resistant HIV Patient Isolates Reveals Patterns of Correlated Mutations in Gag and Protease. - William F. Flynn; Max W. Chang; Zhiqiang Tan; Glenn Oliveira; Jinyun Yuan; Jason F. Okulicz; Bruce E. Torbett; Ronald M. Levy (PLoS Comput. Biol., 2015)

Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015. - Nan-Jie Deng; William F. Flynn; Junchao Xia; R. S. K. Vijayan; Baofeng Zhang; Peng He; Ahmet Mentes; Emilio Gallicchio; Ronald M. Levy (J. Comput. Aided Mol. Des., 2016)

A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge. - Rajat Kumar Pal; Kamran Haider; Divya Kaur; William F. Flynn; Junchao Xia; Ronald M. Levy; Tetiana Taran; Lauren Wickstrom; Tom Kurtzman; Emilio Gallicchio (J. Comput. Aided Mol. Des., 2017)

Erratum to: A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge. - Rajat Kumar Pal; Kamran Haider; Divya Kaur; William F. Flynn; Junchao Xia; Ronald M. Levy; Tetiana Taran; Lauren Wickstrom; Tom Kurtzman; Emilio Gallicchio (J. Comput. Aided Mol. Des., 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. - Robert C. Harris; Nan-Jie Deng; Ronald M. Levy; Ryosuke Ishizuka; Nobuyuki Matubayasi (J. Comput. Chem., 2017)

Improving Prediction Accuracy of Binding Free Energies and Poses of HIV Integrase Complexes Using the Binding Energy Distribution Analysis Method with Flattening Potentials. - Junchao Xia; William F. Flynn; Ronald M. Levy (J. Chem. Inf. Model., 2018)

Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network. - Junchao Xia; William F. Flynn; Emilio Gallicchio; Keith Uplinger; Jonathan D. Armstrong; Stefano Forli; Arthur J. Olson; Ronald M. Levy (J. Chem. Inf. Model., 2019)

Generative Capacity of Probabilistic Protein Sequence Models. - Francisco McGee; Quentin Novinger; Ronald M. Levy; Vincenzo Carnevale; Allan Haldane (CoRR, 2020)

Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses. - Yoshitake Sakae; Bin W. Zhang; Ronald M. Levy; Nan-Jie Deng (J. Comput. Chem., 2020)

Mi3-GPU: MCMC-based inverse Ising inference on GPUs for protein covariation analysis. - Allan Haldane; Ronald M. Levy (Comput. Phys. Commun., 2021)

Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid. - 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 (J. Comput. Aided Mol. Des., 2022)