Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid.

Ronald M. Levy

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. 193-203 2022 36 J. Comput. Aided Mol. Des. 3 https://doi.org/10.1007/s10822-022-00446-5 db/journals/jcamd/jcamd36.html#SunBVCFOCKSDL22

Allan Haldane Ronald M. Levy Mi3-GPU: MCMC-based inverse Ising inference on GPUs for protein covariation analysis. 107312 2021 260 Comput. Phys. Commun. https://doi.org/10.1016/j.cpc.2020.107312 db/journals/cphysics/cphysics260.html#HaldaneL21

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. 56-68 2020 41 J. Comput. Chem. 1 https://doi.org/10.1002/jcc.26078 https://www.wikidata.org/entity/Q90767962 db/journals/jcc/jcc41.html#SakaeZLD20

Francisco McGee Quentin Novinger Ronald M. Levy Vincenzo Carnevale Allan Haldane Generative Capacity of Probabilistic Protein Sequence Models. 2020 abs/2012.02296 CoRR https://arxiv.org/abs/2012.02296 db/journals/corr/corr2012.html#abs-2012-02296

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. 1382-1397 2019 59 J. Chem. Inf. Model. 4 https://doi.org/10.1021/acs.jcim.8b00817 https://www.wikidata.org/entity/Q64111973 db/journals/jcisd/jcisd59.html#XiaFGUAFOL19

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. 1356-1371 2018 58 J. Chem. Inf. Model. 7 https://doi.org/10.1021/acs.jcim.8b00194 https://www.wikidata.org/entity/Q89174818 db/journals/jcisd/jcisd58.html#XiaFL18

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. 29-44 2017 31 J. Comput. Aided Mol. Des. 1 https://doi.org/10.1007/s10822-016-9956-6 https://www.wikidata.org/entity/Q48054359 db/journals/jcamd/jcamd31.html#PalHKFXLTWKG17

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. 45 2017 31 J. Comput. Aided Mol. Des. 1 https://doi.org/10.1007/s10822-016-9987-z https://www.wikidata.org/entity/Q48244185 db/journals/jcamd/jcamd31.html#PalHKFXLTWKG17a

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. 1198-1208 2017 38 J. Comput. Chem. 15 https://doi.org/10.1002/jcc.24668 https://www.wikidata.org/entity/Q48891100 db/journals/jcc/jcc38.html#HarrisDLIM17

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. 743-751 2016 30 J. Comput. Aided Mol. Des. 9 https://doi.org/10.1007/s10822-016-9952-x https://www.wikidata.org/entity/Q39453218 db/journals/jcamd/jcamd30.html#DengFXVZHMGL16

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. 236-246 2015 196 Comput. Phys. Commun. https://doi.org/10.1016/j.cpc.2015.06.010 https://www.wikidata.org/entity/Q28834607 db/journals/cphysics/cphysics196.html#GallicchioXFZSM15

Emilio Gallicchio Haoyuan Chen He Chen Michael Fitzgerald Yang Gao 0019 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. 315-325 2015 29 J. Comput. Aided Mol. Des. 4 https://doi.org/10.1007/s10822-014-9795-2 https://www.wikidata.org/entity/Q36801376 db/journals/jcamd/jcamd29.html#GallicchioCCFGH15

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. 1772-1785 2015 36 J. Comput. Chem. 23 https://doi.org/10.1002/jcc.23996 https://www.wikidata.org/entity/Q27334394 db/journals/jcc/jcc36.html#XiaFGZHTL15

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. 2015 11 PLoS Comput. Biol. 4 https://doi.org/10.1371/journal.pcbi.1004249 https://www.wikidata.org/entity/Q28546549 db/journals/ploscb/ploscb11.html#FlynnCTOYOTL15

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. 475-490 2014 28 J. Comput. Aided Mol. Des. 4 https://doi.org/10.1007/s10822-014-9711-9 https://www.wikidata.org/entity/Q34065423 db/journals/jcamd/jcamd28.html#GallicchioDHWPSFOL14

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. 26:1-26:8 2013 XSEDE https://doi.org/10.1145/2484762.2484830 https://www.wikidata.org/entity/Q104229110 conf/xsede/2013 db/conf/xsede/xsede2013.html#RadakLHRWDGDYLJ13

Emilio Gallicchio Ronald M. Levy Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM). 505-516 2012 26 J. Comput. Aided Mol. Des. 5 https://doi.org/10.1007/s10822-012-9552-3 https://www.wikidata.org/entity/Q36060565 db/journals/jcamd/jcamd26.html#GallicchioL12

Omar Haq Michael Andrec Alexandre V. Morozov Ronald M. Levy Correlated Electrostatic Mutations Provide a Reservoir of Stability in HIV Protease. 2012 8 PLoS Comput. Biol. 9 https://doi.org/10.1371/journal.pcbi.1002675 https://www.wikidata.org/entity/Q28483556 db/journals/ploscb/ploscb8.html#HaqAML12

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. 1986-1998 2011 51 J. Chem. Inf. Model. 8 https://doi.org/10.1021/ci200194w https://www.wikidata.org/entity/Q33945786 db/journals/jcisd/jcisd51.html#FeltsLBPHAPL11

Hisashi Okumura Emilio Gallicchio Ronald M. Levy Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting. 1357-1367 2010 31 J. Comput. Chem. 7 https://doi.org/10.1002/jcc.21419 https://www.wikidata.org/entity/Q33764509 db/journals/jcc/jcc31.html#OkumuraGL10

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. 10 2009 10 BMC Bioinform. S-8 https://doi.org/10.1186/1471-2105-10-S8-S10 https://www.wikidata.org/entity/Q33503921 db/journals/bmcbi/bmcbi10S.html#HaqLMA09

Emilio Gallicchio Ronald M. Levy Manish Parashar Asynchronous replica exchange for molecular simulations. 788-794 2008 29 J. Comput. Chem. 5 https://doi.org/10.1002/jcc.20839 https://www.wikidata.org/entity/Q34296246 db/journals/jcc/jcc29.html#GallicchioLP08

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. 1599-1608 2007 47 J. Chem. Inf. Model. 4 https://doi.org/10.1021/ci7000346 https://www.wikidata.org/entity/Q36900717 db/journals/jcisd/jcisd47.html#ZhouFFL07

Li Zhang Manish Parashar Emilio Gallicchio Ronald M. Levy Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular Dynamics Applications. 127-134 2006 conf/icpp/2006 ICPP https://doi.org/10.1109/ICPP.2006.63 https://doi.ieeecomputersociety.org/10.1109/ICPP.2006.63 db/conf/icpp/icpp2006.html#ZhangPGL06

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). 1752-1780 2005 26 J. Comput. Chem. 16 https://doi.org/10.1002/jcc.20292 https://www.wikidata.org/entity/Q28751619 db/journals/jcc/jcc26.html#BanksBCCDFFHMMMPRZBFGL05

Emilio Gallicchio Ronald M. Levy AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. 479-499 2004 25 J. Comput. Chem. 4 https://doi.org/10.1002/jcc.10400 https://www.wikidata.org/entity/Q54640063 db/journals/jcc/jcc25.html#GallicchioL04

Boris M. Chernyavsky Emilio Gallicchio Doyle D. Knight Ronald M. Levy Andy Page The Rutgers Computational Grid: A Distributed Linux PC Cluster. 267-278 2003 6 Clust. Comput. 3 https://doi.org/10.1023/A:1023544721955 db/journals/cluster/cluster6.html#ChernyavskyGKLP03

Ronald M. Levy Jay Nagarajarao Giovanni Pacifici Mike Spreitzer Asser N. Tantawi Alaa Youssef Performance Management for Cluster Based Web Services. 247-261 2003 conf/im/2003 Integrated Network Management db/conf/im/im2003.html#LevyNPSTY03

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. 517-529 2002 23 J. Comput. Chem. 5 https://doi.org/10.1002/jcc.10045 https://www.wikidata.org/entity/Q48640184 db/journals/jcc/jcc23.html#GallicchioZL02

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. 591-607 2001 22 J. Comput. Chem. 6 https://doi.org/10.1002/jcc.1031 db/journals/jcc/jcc22.html#ZhangGFL01

Boris M. Chernyavsky Emilio Gallicchio Doyle D. Knight Ronald M. Levy The Rutgers Computational Grid Based on Linux PC Cluster. 2001 conf/ppsc/2001 PP db/conf/ppsc/ppsc2001.html#ChernyavskyGKL01

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. 988-1002 2000 16 Bioinform. 11 db/journals/bioinformatics/bioinformatics16.html#WallqvistFMFL00 https://doi.org/10.1093/bioinformatics/16.11.988 https://www.wikidata.org/entity/Q48691396

Dan N. Bernardo Yanbo Ding Karsten Krogh-Jespersen Ronald M. Levy Evaluating Polarizable Potentials on Distributed Memory Parallel Computers: Program Development and Applications. 1141-1152 1995 16 J. Comput. Chem. 9 db/journals/jcc/jcc16.html#BernardoDKL95 https://doi.org/10.1002/jcc.540160908

Steven L. Gallion Ronald M. Levy Paul K. Weiner Fumio Hirata Implementation of a macromolecular mechanics program on a cyber 205 supercomputer. 165-173 1986 10 Comput. Chem. 3 https://doi.org/10.1016/0097-8485(86)80008-0 db/journals/candc/candc10.html#GallionLWH86

Michael Andrec Jonathan D. Armstrong Eddy Arnold Jay L. Banks Joseph D. Bauman Hege S. Beard Dan N. Bernardo Bruce J. Berne Avik Biswas Yixiang X. Cao Vincenzo Carnevale Andres Emanuelli Castaner Max W. Chang Haoyuan Chen He Chen Boris M. Chernyavsky Art E. Cho Pierrick Craveur Wei Dai Wolfgang Damm Nan-Jie Deng Yanbo Ding Addi Fadel Ramy Farid Anthony K. Felts Michael Fitzgerald William F. Flynn Stefano Forli Richard A. Friesner Yoshifumi Fukunishi Emilio Gallicchio Steven L. Gallion Yang Gao 0019 Kamran Haider Allan Haldane Thomas A. Halgren Omar Haq Robert C. Harris Peng He Daniel Himmel Fumio Hirata Ryosuke Ishizuka Shantenu Jha Malathi Kalyanikar Chuan Kao Divya Kaur Karen Kirby Doyle D. Knight Karsten Krogh-Jespersen Tom Kurtzman Krystal LaBarge Tai-Sung Lee Beidi Lu Daniel T. Mainz Jon R. Maple Nobuyuki Matubayasi Francisco McGee Ahmet Mentes Alexandre V. Morozov Lynne Reed Murphy Robert B. Murphy Jay Nagarajarao Yijie Niu Quentin Novinger Jason F. Okulicz Hisashi Okumura Glenn Oliveira Arthur J. Olson Giovanni Pacifici Andy Page Rajat Kumar Pal Manish Parashar Michael A. Parniak Dishaben V. Patel Alex L. PerrymanAlexander L. Perryman Manasi A. Pethe Dean M. Philipp Brian K. Radak Matthew P. Repasky Melissa Romanus Yoshitake Sakae Sade Samlalsingh Daniel N. Santiago Stefan G. Sarafianos Mike Spreitzer Qinfang Sun Zhiqiang Tan Asser N. Tantawi Tetiana Taran Bruce E. Torbett Keith Uplinger R. S. K. Vijayan Anders Wallqvist Ole Weidner Paul K. Weiner Lauren Wickstrom Junchao Xia Darrin M. York Alaa Youssef Jinyun Yuan Baofeng Zhang Bin W. Zhang Li Zhang Linda Yu Zhang Zhiyong Zhou Jie Zhu