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ORCIDRonald M. Levy
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Journal Articles
- 2022
[j29]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): 193-203 (2022)- 2021
- [j28]Allan Haldane, Ronald M. Levy:
Mi3-GPU: MCMC-based inverse Ising inference on GPUs for protein covariation analysis. Comput. Phys. Commun. 260: 107312 (2021) - 2020
- [j27]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): 56-68 (2020) - 2019
- [j26]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): 1382-1397 (2019) - 2018
- [j25]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): 1356-1371 (2018) - 2017
- [j24]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): 29-44 (2017) - [j23]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): 45 (2017) - [j22]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): 1198-1208 (2017) - 2016
- [j21]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): 743-751 (2016) - 2015
- [j20]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: 236-246 (2015) - [j19]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): 315-325 (2015) - [j18]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): 1772-1785 (2015) - [j17]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) - 2014
- [j16]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): 475-490 (2014) - 2012
- [j15]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): 505-516 (2012) - [j14]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) - 2011
- [j13]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): 1986-1998 (2011) - 2010
- [j12]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): 1357-1367 (2010) - 2009
- [j11]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): 10 (2009) - 2008
- [j10]Emilio Gallicchio, Ronald M. Levy, Manish Parashar:
Asynchronous replica exchange for molecular simulations. J. Comput. Chem. 29(5): 788-794 (2008) - 2007
- [j9]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): 1599-1608 (2007) - 2005
- [j8]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): 1752-1780 (2005) - 2004
- [j7]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): 479-499 (2004) - 2003
- [j6]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): 267-278 (2003) - 2002
- [j5]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): 517-529 (2002) - 2001
- [j4]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): 591-607 (2001) - 2000
- [j3]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): 988-1002 (2000) - 1995
- [j2]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): 1141-1152 (1995) - 1986
- [j1]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): 165-173 (1986)
Conference and Workshop Papers
- 2013
- [c4]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: 26:1-26:8 - 2006
- [c3]Li Zhang, Manish Parashar, Emilio Gallicchio, Ronald M. Levy:
Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular Dynamics Applications. ICPP 2006: 127-134 - 2003
- [c2]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: 247-261 - 2001
- [c1]Boris M. Chernyavsky, Emilio Gallicchio, Doyle D. Knight, Ronald M. Levy:
The Rutgers Computational Grid Based on Linux PC Cluster. PP 2001
Informal and Other Publications
- 2020
- [i1]Francisco McGee, Quentin Novinger, Ronald M. Levy, Vincenzo Carnevale, Allan Haldane:
Generative Capacity of Probabilistic Protein Sequence Models. CoRR abs/2012.02296 (2020)
Coauthor Index
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