Ronald M. Levy

34 papers B 1Journal 30Unranked 3

Year	Rank	Type	Title / Venue / Authors
2022	J	`jnl`	Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid. J. Comput. Aided Mol. Des. 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
2021	J	`jnl`	Mi3-GPU: MCMC-based inverse Ising inference on GPUs for protein covariation analysis. Comput. Phys. Commun. Allan Haldane, Ronald M. Levy
2020	J	`jnl`	Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses. J. Comput. Chem. Yoshitake Sakae, Bin W. Zhang, Ronald M. Levy, Nan-Jie Deng
2020	J	`jnl`	Generative Capacity of Probabilistic Protein Sequence Models. CoRR Francisco McGee, Quentin Novinger, Ronald M. Levy, Vincenzo Carnevale, Allan Haldane
2019	J	`jnl`	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. Junchao Xia, William F. Flynn, Emilio Gallicchio, Keith Uplinger, Jonathan D. Armstrong, Stefano Forli, Arthur J. Olson, Ronald M. Levy
2018	J	`jnl`	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. Junchao Xia, William F. Flynn, Ronald M. Levy
2017	J	`jnl`	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. Rajat Kumar Pal, Kamran Haider, Divya Kaur, William F. Flynn, Junchao Xia, Ronald M. Levy, Tetiana Taran, Lauren Wickstrom, Tom Kurtzman, Emilio Gallicchio
2017	J	`jnl`	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. Robert C. Harris, Nan-Jie Deng, Ronald M. Levy, Ryosuke Ishizuka, Nobuyuki Matubayasi
2017	J	`jnl`	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. Rajat Kumar Pal, Kamran Haider, Divya Kaur, William F. Flynn, Junchao Xia, Ronald M. Levy, Tetiana Taran, Lauren Wickstrom, Tom Kurtzman, Emilio Gallicchio
2016	J	`jnl`	Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015. J. Comput. Aided Mol. Des. Nan-Jie Deng, William F. Flynn, Junchao Xia, R. S. K. Vijayan, Baofeng Zhang, Peng He, Ahmet Mentes, Emilio Gallicchio, Ronald M. Levy
2015	J	`jnl`	Asynchronous replica exchange software for grid and heterogeneous computing. Comput. Phys. Commun. Emilio Gallicchio, Junchao Xia, William F. Flynn, Baofeng Zhang, Sade Samlalsingh, Ahmet Mentes, Ronald M. Levy
2015	J	`jnl`	BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge. J. Comput. Aided Mol. Des. 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
2015	J	`jnl`	Deep Sequencing of Protease Inhibitor Resistant HIV Patient Isolates Reveals Patterns of Correlated Mutations in Gag and Protease. PLoS Comput. Biol. William F. Flynn, Max W. Chang, Zhiqiang Tan, Glenn Oliveira, Jinyun Yuan, Jason F. Okulicz, Bruce E. Torbett, Ronald M. Levy
2015	J	`jnl`	Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis. J. Comput. Chem. Junchao Xia, William F. Flynn, Emilio Gallicchio, Bin W. Zhang, Peng He, Zhiqiang Tan, Ronald M. Levy
2014	J	`jnl`	Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge. J. Comput. Aided Mol. Des. Emilio Gallicchio, Nan-Jie Deng, Peng He, Lauren Wickstrom, Alexander L. Perryman, Daniel N. Santiago, Stefano Forli, Arthur J. Olson, Ronald M. Levy
2013	—	`conf`	A framework for flexible and scalable replica-exchange on production distributed CI. XSEDE 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
2012	J	`jnl`	Correlated Electrostatic Mutations Provide a Reservoir of Stability in HIV Protease. PLoS Comput. Biol. Omar Haq, Michael Andrec, Alexandre V. Morozov, Ronald M. Levy
2012	J	`jnl`	Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM). J. Comput. Aided Mol. Des. Emilio Gallicchio, Ronald M. Levy
2011	J	`jnl`	Identification of Alternative Binding Sites for Inhibitors of HIV-1 Ribonuclease H Through Comparative Analysis of Virtual Enrichment Studies. J. Chem. Inf. Model. Anthony K. Felts, Krystal LaBarge, Joseph D. Bauman, Dishaben V. Patel, Daniel Himmel, Eddy Arnold, Michael A. Parniak, Ronald M. Levy
2010	J	`jnl`	Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting. J. Comput. Chem. Hisashi Okumura, Emilio Gallicchio, Ronald M. Levy
2009	J	`jnl`	Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease. BMC Bioinform. Omar Haq, Ronald M. Levy, Alexandre V. Morozov, Michael Andrec
2008	J	`jnl`	Asynchronous replica exchange for molecular simulations. J. Comput. Chem. Emilio Gallicchio, Ronald M. Levy, Manish Parashar
2007	J	`jnl`	Comparative Performance of Several Flexible Docking Programs and Scoring Functions: Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets. J. Chem. Inf. Model. Zhiyong Zhou, Anthony K. Felts, Richard A. Friesner, Ronald M. Levy
2006	B	`conf`	Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular Dynamics Applications. ICPP Li Zhang, Manish Parashar, Emilio Gallicchio, Ronald M. Levy
2005	J	`jnl`	Integrated Modeling Program, Applied Chemical Theory (IMPACT). J. Comput. Chem. 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
2004	J	`jnl`	AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. J. Comput. Chem. Emilio Gallicchio, Ronald M. Levy
2003	—	`conf`	Performance Management for Cluster Based Web Services. Integrated Network Management Ronald M. Levy, Jay Nagarajarao, Giovanni Pacifici, Mike Spreitzer, Asser N. Tantawi, Alaa Youssef
2003	J	`jnl`	The Rutgers Computational Grid: A Distributed Linux PC Cluster. Clust. Comput. Boris M. Chernyavsky, Emilio Gallicchio, Doyle D. Knight, Ronald M. Levy, Andy Page
2002	J	`jnl`	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. Emilio Gallicchio, Linda Yu Zhang, Ronald M. Levy
2001	J	`jnl`	Solvent models for protein-ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations. J. Comput. Chem. Linda Yu Zhang, Emilio Gallicchio, Richard A. Friesner, Ronald M. Levy
2001	—	`conf`	The Rutgers Computational Grid Based on Linux PC Cluster. PP Boris M. Chernyavsky, Emilio Gallicchio, Doyle D. Knight, Ronald M. Levy
2000	J	`jnl`	Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases. Bioinform. Anders Wallqvist, Yoshifumi Fukunishi, Lynne Reed Murphy, Addi Fadel, Ronald M. Levy
1995	J	`jnl`	Evaluating Polarizable Potentials on Distributed Memory Parallel Computers: Program Development and Applications. J. Comput. Chem. Dan N. Bernardo, Yanbo Ding, Karsten Krogh-Jespersen, Ronald M. Levy
1986	J	`jnl`	Implementation of a macromolecular mechanics program on a cyber 205 supercomputer. Comput. Chem. Steven L. Gallion, Ronald M. Levy, Paul K. Weiner, Fumio Hirata