R. Levy

发表

Quasi‐harmonic method for studying very low frequency modes in proteins

A. R. Srinivasan, J. Mccammon, R. Levy, 1984, Biopolymers.

Inference of signaling and gene regulatory networks by steady-state perturbation experiments: structure and accuracy.

Eduardo Sontag, B. Kholodenko, R. Levy, 2005, Journal of theoretical biology.

Protein folding pathways from replica exchange simulations and a kinetic network model.

R. Levy, M. Andrec, A. K. Felts, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Simplified amino acid alphabets for protein fold recognition and implications for folding.

R. Levy, A. Wallqvist, L. Murphy, 2000, Protein engineering.

Potts Hamiltonian models of protein co-variation, free energy landscapes, and evolutionary fitness.

R. Levy, A. Haldane, W. Flynn, 2017, Current opinion in structural biology.

Influence of multiple-sequence-alignment depth on Potts statistical models of protein covariation.

R. Levy, A. Haldane, 2018, Physical review. E.

Theory of binless multi-state free energy estimation with applications to protein-ligand binding.

Z. Tan, R. Levy, E. Gallicchio, 2012, The Journal of chemical physics.

Direct Determination of Kinetic Rates from Single-Molecule Photon Arrival Trajectories Using Hidden Markov Models.

R. Levy, M. Andrec, D. Talaga, 2003, The journal of physical chemistry. A.

Large scale simulation of macromolecules in solution: Combining the periodic fast multipole method with multiple time step integrators

B. Berne, R. Levy, R. Zhou, 1997 .

Conformational equilibria and free energy profiles for the allosteric transition of the ribose-binding protein.

Emilio Gallicchio, Ronald M Levy, R. Levy, 2005, Journal of molecular biology.

Intrinsic pKas of ionizable residues in proteins: An explicit solvent calculation for lysozyme

R. Levy, F. Figueirido, G. S. Del Buono, 1994, Proteins.

Simulating replica exchange simulations of protein folding with a kinetic network model

R. Levy, M. Andrec, E. Gallicchio, 2007, Proceedings of the National Academy of Sciences.

An Anisotropic Polarizable Water Model: Incorporation of All-Atom Polarizabilities into Molecular Mechanics Force Fields

Dan N. Bernardo, R. Levy, Yanbo Ding, 1994 .

The linear interaction energy method for the prediction of protein stability changes upon mutation

R. Levy, E. Gallicchio, L. Wickstrom, 2012, Proteins.

Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects.

R. Levy, E. Gallicchio, Emilio Gallicchio, 1998, Annual review of physical chemistry.

Enthalpy−Entropy and Cavity Decomposition of Alkane Hydration Free Energies: Numerical Results and Implications for Theories of Hydrophobic Solvation

R. Levy, E. Gallicchio, A. Kubo, 2000 .

Large scale affinity calculations of cyclodextrin host-guest complexes: Understanding the role of reorganization in the molecular recognition process.

R. Levy, E. Gallicchio, L. Wickstrom, 2013, Journal of chemical theory and computation.

Parameterization of an effective potential for protein–ligand binding from host–guest affinity data

M. Gilson, R. Levy, E. Gallicchio, 2016, Journal of molecular recognition : JMR.

Evaluation of the configurational entropy for proteins: application to molecular dynamics simulations of an α-helix

M. Karplus, J. Kushick, R. Levy, 1984 .

Conformational Analysis of the DFG-Out Kinase Motif and Biochemical Profiling of Structurally Validated Type II Inhibitors

Roland L. Dunbrack, R. Levy, Haiching Ma, 2014, Journal of medicinal chemistry.

Simple continuous and discrete models for simulating replica exchange simulations of protein folding.

R. Levy, M. Andrec, E. Gallicchio, 2008, The journal of physical chemistry. B.

Free Energy Surfaces of -Hairpin and -Helical Peptides Generated by Replica Exchange Molecular Dynamics with the AGBNP Implicit Solvent Model

Anthony K. Felts, R. Levy, A. K. Felts, 2004 .

Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model.

Anthony K. Felts, R. Levy, A. K. Felts, 2004, Proteins: Structure, Function, and Bioinformatics.

Structural propensities of kinase family proteins from a Potts model of residue co‐variation

R. Levy, A. Haldane, W. Flynn, 2016, Protein science : a publication of the Protein Society.

Conformational landscape of the human immunodeficiency virus type 1 reverse transcriptase non-nucleoside inhibitor binding pocket: lessons for inhibitor design from a cluster analysis of many crystal structures.

Omar Haq, Ronald M Levy, Anthony K Felts, 2009, Journal of medicinal chemistry.

Relationship between Solvation Thermodynamics from IST and DFT Perspectives.

Bin W. Zhang, R. Levy, N. Matubayasi, 2017, The journal of physical chemistry. B.

Comparative Performance of Several Flexible Docking Programs and Scoring Functions: Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets.

Richard A. Friesner, Anthony K. Felts, Ronald M. Levy, 2007 .

On finite‐size effects in computer simulations using the Ewald potential

Ronald M. Levy, R. Levy, F. Figueirido, 1995 .

Computer simulations of the dielectric properties of water: Studies of the simple point charge and transferrable intermolecular potential models

Ronald M. Levy, R. Levy, H. Alper, 1989 .

Conserving energy during molecular dynamics simulations of water, proteins, and proteins in water

Fumio Hirata, Martin Yarmush, R. Levy, 1990 .

Gaussian fluctuation formula for electrostatic free‐energy changes in solution

Ronald M. Levy, Douglas B. Kitchen, R. Levy, 1991 .

Solvent effects on the adiabatic free energy difference between the ground and excited states of methylindole in water

R. Levy, J. Westbrook, D. Kitchen, 1991 .

Molecular dynamics simulations of water with Ewald summation for the long range electrostatic interactions

Ronald M. Levy, R. Levy, H. Alper, 1991 .

Molecular dynamics simulation of solvated protein at high pressure.

R. Levy, D. Kitchen, R M Levy, 1992, Biochemistry.

Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling.

Richard A Friesner, Jennifer L. Knight, Emilio Gallicchio, 2008, Acta crystallographica. Section D, Biological crystallography.

Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction

Yuichi Harano, Richard A. Friesner, Ronald M. Levy, 2004, Journal of Structural and Functional Genomics.

Effect of anisotropy and anharmonicity on protein crystallographic refinement. An evaluation by molecular dynamics.

M Karplus, J Kuriyan, G A Petsko, 1986, Journal of molecular biology.

Protein hydration and unfolding--insights from experimental partial specific volumes and unfolded protein models.

R. Levy, L. Murphy, N. Matubayasi, 1998, Folding & design.

Antibacterial peptide microcin J25 inhibits transcription by binding within and obstructing the RNA polymerase secondary channel.

Jennifer L. Knight, Ronald M Levy, Jayanta Mukhopadhyay, 2004, Molecular cell.

Estimation of dynamic parameters from NMR relaxation data using the Lipari-Szabo model-free approach and Bayesian statistical methods.

G T Montelione, G. Montelione, R. Levy, 1999, Journal of magnetic resonance.

Propagation of experimental uncertainties using the Lipari-Szabo model-free analysis of protein dynamics

Ronald M. Levy, Michael Andrec, Gaetano T. Montelione, 1998, Journal of biomolecular NMR.

A large data set comparison of protein structures determined by crystallography and NMR: Statistical test for structural differences and the effect of crystal packing

Michael Andrec, Jasmine Young, Gaetano T Montelione, 2007, Proteins.

a-Helix dipole model and electrostatic stabilization of 4-a-helical proteins

R. Sheridan, R. Levy, F. R. SALEMMEt, 2022 .

Diffusive langevin dynamics of model alkanes

J. Andrew McCammon, Ronald M. Levy, Martin Karplus, 1979 .

Ligand Binding Thermodynamic Cycles: Hysteresis, the Locally Weighted Histogram Analysis Method, and the Overlapping States Matrix

Bin W. Zhang, Z. Tan, R. Levy, 2019, Journal of Chemical Theory and Computation.

Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation.

R. Levy, E. Gallicchio, R. Vijayan, 2016, Journal of chemical theory and computation.

Solvation Thermodynamics from the Perspective of Endpoints DFT.

Bin W. Zhang, R. Levy, N. Matubayasi, 2020, The journal of physical chemistry. B.

Spatially-Decomposed Free Energy of Solvation Based on the Endpoint Density-Functional Method.

Bin W. Zhang, R. Levy, N. Matubayasi, 2019, Journal of chemical theory and computation.

The Role of Interfacial Water in Protein-Ligand Binding: Insights from the Indirect Solvent Mediated Potential of Mean Force.

Bin W. Zhang, R. Levy, N. Matubayasi, 2018, Journal of chemical theory and computation.

HIV-1 integrase tetramers are the antiviral target of pyridine-based allosteric integrase inhibitors

A. Engelman, R. Levy, D. Lyumkis, 2019, eLife.

Increase of carbon-13 NMR relaxation times in proteins due to picosecond motional averaging

M. Karplus, J. Mccammon, R. Levy, 1981 .

Molecular dynamics study of non-nucleoside reverse transcriptase inhibitor 4-[[4-[[4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl]amino]-2-pyrimidinyl]amino]benzonitrile (TMC278/rilpivirine) aggregates: correlation between amphiphilic properties of the drug and oral bioavailability.

Emilio Gallicchio, Ronald M Levy, Eddy Arnold, 2009, Journal of medicinal chemistry.

Antigenic characteristics of rhinovirus chimeras designed in silico for enhanced presentation of HIV-1 gp41 epitopes [corrected].

R. Levy, E. Gallicchio, E. Arnold, 2010, Journal of molecular biology.

Antigenic Characteristics of Rhinovirus Chimeras Designed in silico for En 5 hanced Presentation of HIV-1 gp 41 Epitopes

R. Levy, E. Gallicchio, E. Arnold, 2010 .

Thermodynamics of the Hydration Shell. 2. Excess Volume and Compressibility of a Hydrophobic Solute

R. Levy, Nobuyuki Matubayasi and, 1996 .

On the local and nonlocal components of solvation thermodynamics and their relation to solvation shell models

R. Levy, E. Gallicchio, N. Matubayasi, 1998 .

Inference of Epistatic Effects Leading to Entrenchment and Drug Resistance in HIV-1 Protease

R. Levy, B. Torbett, A. Haldane, 2016, bioRxiv.

Inference of Epistatic Effects Leading to Entrenchment and Drug Resistance in HIV-1 Protease

R. Levy, B. Torbett, A. Haldane, 2016, bioRxiv.

Variable quadratic propagator for quantum Monte Carlo simulations

R. Friesner, R. Levy, Peisen Zhang, 1988 .

Implicit solvent models for protein-ligand binding: Insights based on explicit solvent simulations

R. Levy, E. Gallicchio, L. Y. Zhang, 1999 .

Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.

Bin W. Zhang, R. Levy, N. Deng, 2015, Journal of chemical theory and computation.

Coevolutionary Landscape of Kinase Family Proteins: Sequence Probabilities and Functional Motifs.

R. Levy, A. Haldane, W. Flynn, 2018, Biophysical journal.

Field strength dependence of dielectric saturation in liquid water

R. Levy, H. Alper, 1990 .

Ligand Binding Thermodynamic Cycles: Hysteresis, LWHAM, and the Overlapping States Matrix.

Bin W. Zhang, Z. Tan, R. Levy, 2019, Journal of Chemical Theory and Computation.

Molecular Dynamics of the Proline Switch and Its Role in Crk Signaling

R. Levy, J. Xia, 2014, The journal of physical chemistry. B.

Vibrational relaxation and Bloch–Redfield theory

R. Levy, F. Figueirido, Francisco Figueirido, 1992 .

Molecular dynamics simulation of time-resolved fluorescence and nonequilibrium solvation of formaldehyde in water

R. Levy, D. Kitchen, K. Krogh-Jespersen, 1990 .

Distinguishing Binders from False Positives by Free Energy Calculations: Fragment Screening Against the Flap Site of HIV Protease

Arthur J. Olson, Lauren Wickstrom, Stefano Forli, 2014, The journal of physical chemistry. B.

Determination of Protein Structures in Solution Using Nmr Data and Impact

R. Levy, A. Pardi, D. Kitchen, 1988 .

Epistasis and entrenchment of drug resistance in HIV-1 subtype B

R. Levy, E. Arnold, A. Haldane, 2019, eLife.

Trajectory Studies of in Flexible Molecules NMR Relaxation

R. Levy, 2009 .

The AGBNP2 Implicit Solvation Model.

R. Levy, E. Gallicchio, K. Paris, 2009, Journal of chemical theory and computation.

Erratum: “Large scale simulation of macromolecules in solution: Combining the periodic fast multipole method with multiple time step integrators” [J. Chem. Phys. 106, 9835 (1997)]

B. Berne, R. Levy, R. Zhou, 1997 .

Monte Carlo Study of the Effect of Pressure on Hydrophobic Association

R. Levy, N. Matubayasi, V. Payne, 1997 .

HIV-1 reverse transcriptase structure with RNase H inhibitor dihydroxy benzoyl naphthyl hydrazone bound at a novel site.

Jennifer L. Knight, A. D. Clark, R. Levy, 2006, ACS chemical biology.

Molecular electrostatic potentials and partial atomic charges from correlated wave functions: Applications to the electronic ground and excited states of 3‐methylindole

R. Levy, J. Westbrook, K. Krogh-Jespersen, 1992 .

On finite‐size effects in computer simulations using the Ewald potential

R. Levy, F. Figueirido, Gabriela S. Del Buono, 1995, chem-ph/9505001.

Exploring the Free-Energy Landscape and Thermodynamics of Protein-Protein Association.

R. Levy, E. Gallicchio, L. Wickstrom, 2020, Biophysical journal.

Computational design of small molecular modulators of protein–protein interactions with a novel thermodynamic cycle: Allosteric inhibitors of HIV‐1 integrase

R. Levy, R. Vijayan, N. Deng, 2020, Protein science : a publication of the Protein Society.

Ionic association in methanol and related solvents: an extended RISM analysis

R. Levy, F. Hirata, 1987 .

Large‐Scale Asynchronous and Distributed Multidimensional Replica Exchange Molecular Simulations and Efficiency Analysis

Bin W. Zhang, Z. Tan, R. Levy, 2016, Journal of computational chemistry.

AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high‐resolution modeling

Ronald M. Levy, Emilio Gallicchio, R. Levy, 2004, J. Comput. Chem..

Protein Folding and Binding: Effective Potentials, Replica Exchange Simulations, and Network Models

Anthony K. Felts, Ronald M. Levy, Michael Andrec, 2009 .

Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling.

Richard A Friesner, Anthony K. Felts, Emilio Gallicchio, 2008, Journal of chemical theory and computation.

Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases

Ronald M. Levy, Anders Wallqvist, Yoshifumi Fukunishi, 2000, Bioinform..

Vibrational approach to the dynamics of an α‐helix

Ronald M. Levy, Martin Karplus, M. Karplus, 1979 .

Chloride Ion Hydration and Diffusion in Supercritical Water Using a Polarizable Water Model

P. Rossky, R. Levy, N. Matubayasi, 2002 .

Initial fluorescence depolarization of tyrosines in proteins

R. Levy, A. Szabó, 1982 .

Distance-restrained docking of rifampicin and rifamycin SV to RNA polymerase using systematic FRET measurements: developing benchmarks of model quality and reliability.

Jennifer L. Knight, Ronald M Levy, Jayanta Mukhopadhyay, 2005, Biophysical journal.

NMR relaxation parameters in molecules with internal motion: exact Langevin trajectory results compared with simplified relaxation models

Ronald M. Levy, Peter G. Wolynes, Martin Karplus, 1981 .

Structural Organization of Bacterial RNA Polymerase Holoenzyme and the RNA Polymerase-Promoter Open Complex

Jennifer L. Knight, R. Ebright, R. Levy, 2002, Cell.

NMR relaxation in proteins with fast internal motions and slow conformational exchange: model-free framework and Markov state simulations.

Junchao Xia, Ronald M Levy, R. Levy, 2013, The journal of physical chemistry. B.

Entropy−Enthalpy Compensation in Solvation and Ligand Binding Revisited

Ronald M. Levy, Emilio Gallicchio, R. Levy, 1998 .

Integrated Modeling Program, Applied Chemical Theory (IMPACT)

Richard A. Friesner, Anthony K. Felts, Ronald M. Levy, 2005, J. Comput. Chem..

Simple models for solvation effects on electronic transition energies: Formaldehyde and water

R. Levy, J. Westbrook, K. Krogh-Jespersen, 1989 .

Protein dynamics and NMR relaxation: comparison of simulations with experiment

R. Levy, A. Szabó, G. Lipari, 1982, Nature.

Computer Simulations of Macromolecular Dynamics: Models for Vibrational Spectroscopy and X‐Ray Refinement a

R. Levy, R M Levy, 1986, Annals of the New York Academy of Sciences.

Combined effect of restricted rotational diffusion plus jumps on nuclear magnetic resonance and fluorescence probes of aromatic ring motions in proteins.

R. Sheridan, R. Levy, 1983, Biophysical journal.

Determining local conformational variations in DNA. Nuclear magnetic resonance structures of the DNA duplexes d(CGCCTAATCG) and d(CGTCACGCGC) generated using back-calculation of the nuclear Overhauser effect spectra, a distance geometry algorithm and constrained molecular dynamics.

R. Levy, A. Pardi, D. Kitchen, 1990, Journal of molecular biology.

Investigation of the Polymeric Properties of α-Synuclein and Comparison with NMR Experiments: A Replica Exchange Molecular Dynamics Study.

Ronald M Levy, R. Levy, J. Baum, 2012, Journal of chemical theory and computation.

Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all‐atom force field and the surface generalized born solvent model

Anthony K. Felts, R. Levy, A. K. Felts, 2002, Proteins.

The mechanism of H171T resistance reveals the importance of Nδ-protonated His171 for the binding of allosteric inhibitor BI-D to HIV-1 integrase

A. Engelman, R. Levy, E. Poeschla, 2014, Retrovirology.

The mechanism of H171T resistance reveals the importance of Nδ-protonated His171 for the binding of allosteric inhibitor BI-D to HIV-1 integrase

A. Engelman, R. Levy, E. Poeschla, 2014, Retrovirology.

The transition between active and inactive conformations of Abl kinase studied by rock climbing and Milestoning.

N. Buchete, R. Elber, R. Levy, 2019, Biochimica et biophysica acta. General subjects.

Quasi-harmonic method for calculating vibrational spectra from classical simulations on multi-dimensional anharmonic potential surfaces

Richard A. Friesner, Ronald M. Levy, R. Friesner, 1984 .

Molecular dynamics of an a-helical polypeptide: Temperature dependence and deviation from harmonic behavior (protein dynamics/temperature factor/quantum corrections/fluctuations/normal modes)

Ronald M. Levy, David Perahia, Martin Karplus, 1982 .

Advances in all atom sampling methods for modeling protein-ligand binding affinities.

Emilio Gallicchio, Ronald M Levy, R. Levy, 2011, Current opinion in structural biology.

Deep Sequencing of Protease Inhibitor Resistant HIV Patient Isolates Reveals Patterns of Correlated Mutations in Gag and Protease

Zhiqiang Tan, Ronald M. Levy, Jinyun Yuan, 2015, PLoS Comput. Biol..

Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease

Ronald M. Levy, Omar Haq, Alexandre V. Morozov, 2009, BMC Bioinformatics.

Chimeric Rhinoviruses Displaying MPER Epitopes Elicit Anti-HIV Neutralizing Responses

R. Levy, E. Gallicchio, E. Arnold, 2013, PloS one.

Three-dimensional structure of echistatin and dynamics of the active site

R. Levy, D. Kominos, V. Garsky, 1994, Journal of biomolecular NMR.

A Bayesian statistical method for the detection and quantification of rotational diffusion anisotropy from NMR relaxation data.

D. Weber, G. Montelione, R. Levy, 2000, Journal of magnetic resonance.

Crankshaft motions of the polypeptide backbone in molecular dynamics simulations of human type-α transforming growth factor

G T Montelione, G. Montelione, R. Levy, 1995, Journal of biomolecular NMR.

Using Macromolecular Dynamics Simulations to Interpret Experiments

R. Levy, 1986 .

alpha-Helix dipole model and electrostatic stabilization of 4-alpha-helical proteins.

F R Salemme, R. Sheridan, R. Levy, 1982, Proceedings of the National Academy of Sciences of the United States of America.

Molecular Dynamics Free Energy Simulations Reveal the Mechanism for the Antiviral Resistance of the M66I HIV-1 Capsid Mutation

R. Levy, S. Sarafianos, N. Deng, 2021, Viruses.

Induction of contractile activity by rigor complexes in myofibrils.

R. Levy, M. Kushmerick, 1977, Biochemical and biophysical research communications.

Ca2+ dependence of tension and ADP production in segments of chemically skinned muscle fibers.

R. Levy, M. Kushmerick, Y. Umazume, 1976, Biochimica et biophysica acta.

Analysis of side‐chain conformational distributions in neutrophil peptide‐5 nmr structures

R. Levy, A. Pardi, D. Kominos, 1990, Biopolymers.

Solution structures of proteins from NMR data and modeling: alternative folds for neutrophil peptide 5.

R. Levy, A. Pardi, D. Kitchen, 1989, Biochemistry.

A combined treatment of hydration and dynamical effects for the modeling of host–guest binding thermodynamics: the SAMPL5 blinded challenge

Lauren Wickstrom, Rajat Kumar Pal, Ronald M. Levy, 2016, Journal of Computer-Aided Molecular Design.

The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators

Ronald M. Levy, Emilio Gallicchio, Linda Yu Zhang, 2002, J. Comput. Chem..

Fold Recognition using the OPLS All-Atom Potential and the Surface Generalized Born Solvent Model

Anthony K. Felts, R. Levy, A. K. Felts, 2002 .

Solvent models for protein–ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations

Richard A. Friesner, Ronald M. Levy, Emilio Gallicchio, 2001, J. Comput. Chem..

Recent theoretical and computational advances for modeling protein-ligand binding affinities.

Emilio Gallicchio, Ronald M Levy, R. Levy, 2011, Advances in protein chemistry and structural biology.

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, 2011, J. Chem. Inf. Model..

Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update.

Ronald M Levy, Peicheng Du, Michael Andrec, 2003, Protein engineering.

On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy.

Emilio Gallicchio, Ronald M Levy, Anthony K Felts, 2003, Journal of the American Chemical Society.

Structural reorganization of alpha-synuclein at low pH observed by NMR and REMD simulations.

Ronald M Levy, R. Levy, J. Baum, 2009, Journal of molecular biology.

Asynchronous replica exchange software for grid and heterogeneous computing

Baofeng Zhang, Ronald M. Levy, Emilio Gallicchio, 2015, Comput. Phys. Commun..

Structural Reorganization of α-Synuclein at Low pH Observed by NMR and REMD Simulations

Ronald M. Levy, R. Levy, J. Baum, 2009 .

Motional averaging of proton nuclear Overhauser effects in proteins. Predictions from a molecular dynamics simulation of lysozyme

M. Karplus, C. Dobson, R. Levy, 1984 .

Corrections to the quasiharmonic approximation for evaluating molecular entropies

R. Levy, A. Szabó, O. Rojas, 1986 .

The Rutgers Computational Grid: A Distributed Linux PC Cluster

Ronald M. Levy, Doyle D. Knight, Emilio Gallicchio, 2003, Cluster Computing.

The UWHAM and SWHAM Software Package

Bin W. Zhang, R. Levy, Shima Arasteh, 2019, Scientific Reports.

The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities.

Emilio Gallicchio, Ronald M Levy, R. Levy, 2010, Journal of chemical theory and computation.

Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit.

Zhiqiang Tan, Peng He, Emilio Gallicchio, 2016, The journal of physical chemistry. B.

New Linear Interaction Method for Binding Affinity Calculations Using a Continuum Solvent Model

Ruhong Zhou, Richard A. Friesner, Ronald M. Levy, 2001 .

Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations.

Michael Andrec, Emilio Gallicchio, Ronald M Levy, 2011, The journal of physical chemistry. B.

M. Karplus, J. Mccammon, R. Levy, 1981 .

A Model for Studying Drying at Hydrophobic Interfaces: Structural and Thermodynamic Properties†

R. Levy, A. Wallqvist, and Emilio Gallicchio, 2001 .

The generative capacity of probabilistic protein sequence models

Slobodan Vucetic, Allan Haldane, Francisco McGee, 2020, Nature Communications.

How kinetics within the unfolded state affects protein folding: an analysis based on markov state models and an ultra-long MD trajectory.

Ronald M Levy, R. Levy, Nan-jie Deng, 2013, The journal of physical chemistry. B.

A Stochastic Solution to the Unbinned WHAM Equations.

Zhiqiang Tan, Bin W Zhang, Junchao Xia, 2015, The journal of physical chemistry letters.

Motions of an α‐helical polypeptide: Comparison of molecular and harmonic dynamics

Ronald M. Levy, David Perahia, M. Karplus, 1990 .

Temperature-dependent molecular dynamics and restrained X-ray refinement simulations of a Z-DNA hexamer.

P. Weiner, R. Levy, E. Westhof, 1986, Journal of molecular biology.

Dipolar NMR relaxation of nonprotonated aromatic carbons in proteins. Structural and dynamical effects.

M. Karplus, C. Dobson, R. Levy, 1982, Biophysical journal.

MOLECULAR DYNAMICS OF MYOGLOBIN AT 2980K Results from a 300-ps Computer Simulation

M. Karplus, R. Sheridan, R. Levy, 2005 .

Helix–coil transitions in a simple polypeptide model

Ronald M. Levy, J. A. McCammon, Martin Karplus, 1980 .

PrimeX and the Schrödinger computational chemistry suite of programs

Ronald M. Levy, Zhiyong Zhou, Emilio Gallicchio, 2012 .

Large scale free energy calculations for blind predictions of protein–ligand binding: the D3R Grand Challenge 2015

Baofeng Zhang, Peng He, Ronald M. Levy, 2016, Journal of Computer-Aided Molecular Design.

Protein Loop Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates.

Bin W. Zhang, R. Levy, Shima Arasteh, 2021, The journal of physical chemistry letters.

Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates.

Bin W. Zhang, R. Levy, Robert Abel, 2018, The journal of physical chemistry letters.

The role of epistasis in determining the fitness landscape of HIV proteins

R. Levy, A. Haldane, A. Biswas, 2021, bioRxiv.

Unique Features of Different Classes of G-Protein-Coupled Receptors Revealed from Sequence Coevolutionary and Structural Analysis

R. Levy, A. Haldane, Y. Miao, 2021, bioRxiv.

Ronald M. Levy, Omar Haq, Alexandre V. Morozov, 2012, PLoS Comput. Biol..

A New Class of Allosteric HIV-1 Integrase Inhibitors Identified by Crystallographic Fragment Screening of the Catalytic Core Domain*

A. Engelman, Erik Serrao, R. Levy, 2016, The Journal of Biological Chemistry.

Allosteric HIV‐1 integrase inhibitors promote aberrant protein multimerization by directly mediating inter‐subunit interactions: Structural and thermodynamic modeling studies

A. Engelman, R. Levy, M. Kvaratskhelia, 2016, Protein science : a publication of the Protein Society.

Protein backbone structure determination using only residual dipolar couplings from one ordering medium

R. Levy, M. Andrec, R M Levy, 2001, Journal of biomolecular NMR.

Protein structural motif recognition via NMR residual dipolar couplings.

R. Levy, M. Andrec, R M Levy, 2001, Journal of the American Chemical Society.

Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses

Bin W Zhang, Ronald M Levy, Bin W. Zhang, 2020, J. Comput. Chem..

Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations.

Ronald M Levy, Weihua Zheng, R. Levy, 2011, Journal of the American Chemical Society.

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

Nobuyuki Matubayasi, Ryosuke Ishizuka, Ronald M. Levy, 2017, J. Comput. Chem..

Viewing the born model for ion hydration through a microscope

R. Levy, F. Hirata, P. Redfern, 1988 .

Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network

Stefano Forli, Emilio Gallicchio, Junchao Xia, 2019, J. Chem. Inf. Model..

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, Ronald M Levy, William Flynn, 2018, J. Chem. Inf. Model..

Large‐scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis

Peng He, Zhiqiang Tan, Ronald M. Levy, 2015, J. Comput. Chem..

Asynchronous replica exchange for molecular simulations

Manish Parashar, Ronald M. Levy, Emilio Gallicchio, 2008, J. Comput. Chem..

On Finite-Size Corrections to the Free Energy of Ionic Hydration

Ronald M. Levy, A. Buono, R. Levy, 1997 .

Dielectric and thermodynamic response of a generalized reaction field model for liquid state simulations

Ronald M. Levy, R. Levy, H. Alper, 1993 .

Protein sequential resonance assignments by combinatorial enumeration using 13Cα chemical shifts and their (i, i−1) sequential connectivities

Ronald M. Levy, Michael Andrec, R. Levy, 2002, Journal of biomolecular NMR.

Solvent effects on the torsional dynamics of a twisted intramolecular charge transfer (TICT) molecule: bianthryl in acetonitrile

R. Levy, K. Krogh-Jespersen, Maureen J. Smith, 1993 .

Estimation of interatomic distances in proteins from NOE spectra at longer mixing times using an empirical two-spin equation

R. Levy, A. K. Suri, 1993 .

Thermodynamics of the Hydration Shell. 1. Excess Energy of a Hydrophobic Solute

R. Levy, N. Matubayasi, L. H. Reed, 1994 .

In silico vaccine design based on molecular simulations of rhinovirus chimeras presenting HIV-1 gp41 epitopes.

Emilio Gallicchio, Ronald M Levy, Eddy Arnold, 2009, Journal of molecular biology.

BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge

Jie Zhu, He Chen, Yang Gao, 2015, Journal of Computer-Aided Molecular Design.

Comparative Performance of Several Flexible Docking Programs and Scoring Functions: Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets

Richard A. Friesner, Anthony K. Felts, Ronald M. Levy, 2007, J. Chem. Inf. Model..

Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation.

Bin W. Zhang, Z. Tan, R. Levy, 2016, The Journal of chemical physics.

First Passage Times, Lifetimes, and Relaxation Times of Unfolded Proteins.

Anirvan M. Sengupta, R. Levy, Wei Dai, 2015, Physical review letters.

Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM)

Ronald M. Levy, Emilio Gallicchio, R. Levy, 2012, Journal of Computer-Aided Molecular Design.

Temperature weighted histogram analysis method, replica exchange, and transition paths.

Anthony K. Felts, Michael Andrec, Emilio Gallicchio, 2005, The journal of physical chemistry. B.

Exploring the Free Energy Landscape and Thermodynamics of Protein-Protein Association: HIV-1 Integrase Multimerization Induced by an Allosteric Inhibitor

R. Levy, L. Wickstrom, M. Kvaratskhelia, 2020, bioRxiv.

Global folding of proteins using a limited number of distance constraints.

R. Levy, D. Kominos, R M Levy, 1993, Protein engineering.

Evaluating polarizable potentials on distributed memory parallel computers: Program development and applications

Ronald M. Levy, Karsten Krogh-Jespersen, Dan N. Bernardo, 1995, J. Comput. Chem..

SOLVATION FREE ENERGIES OF SMALL AMIDES AND AMINES FROM MOLECULAR DYNAMICS/FREE ENERGY PERTURBATION SIMULATIONS USING PAIRWISE ADDITIVE AND MANY-BODY POLARIZABLE POTENTIALS

Ronald M. Levy, Karsten Krogh-Jespersen, Dan N. Bernardo, 1995 .

HIV-1 Integrase Tetramers are the Antiviral Target of Pyridine-based Allosteric Integrase 1 Inhibitors 2 3

A. Engelman, R. Levy, D. Lyumkis, 2022 .

Solvent effects on optical absorption spectra: the 1A1 .fwdarw. 1A2 transition of formaldehyde in water

R. Levy, K. Krogh-Jespersen, J. T. Blair, 1989 .

Recovering kinetics from a simplified protein folding model using replica exchange simulations: a kinetic network and effective stochastic dynamics.

Michael Andrec, Emilio Gallicchio, Ronald M Levy, 2009, The journal of physical chemistry. B.

Thermodynamic Decomposition of Hydration Free Energies by Computer Simulation: Application to Amines, Oxides, and Sulfides

Ronald M. Levy, R. Levy, Masahito Mogami Kubo, 1997 .

Molecular dynamics of myoglobin at 298 degrees K. Results from a 300-ps computer simulation.

M Karplus, M. Karplus, S. Swaminathan, 1985, Biophysical journal.

The UWHAM and SWHAM Software Package

Bin W Zhang, Ronald M Levy, Bin W. Zhang, 2019, Scientific Reports.

Structural reorganization of alpha-synuclein at low pH observed by NMR and REMD simulations.

R. Levy, J. Baum, Kuen-Phon Wu, 2009, Journal of molecular biology.

The Excess Chemical Potential of Water at the Interface with a Protein from End Point Simulations.

Bin W. Zhang, R. Levy, N. Matubayasi, 2018, The journal of physical chemistry. B.

Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations.

R. Levy, Weihua Zheng, N. Deng, 2011, Journal of the American Chemical Society.

A new RISM integral equation for solvated polymers

R. Levy, F. Hirata, 1987 .

Comparing alchemical and physical pathway methods for computing the absolute binding free energy of charged ligands.

Bin W Zhang, Junchao Xia, Bin W. Zhang, 2018, Physical chemistry chemical physics : PCCP.

Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge

Arthur J. Olson, Lauren Wickstrom, Alex L. Perryman, 2014, Journal of Computer-Aided Molecular Design.

Conformational populations of ligand‐sized molecules by replica exchange molecular dynamics and temperature reweighting

Ronald M. Levy, Emilio Gallicchio, Hisashi Okumura, 2009, J. Comput. Chem..

Recent theoretical and computational advances for modeling protein-ligand binding affinities.

R. Levy, Emilio Gallicchio, 2011, Advances in protein chemistry and structural biology.

Anthony K. Felts, R. Levy, E. Arnold, 2009, Journal of medicinal chemistry.

Conformational equilibrium of cytochrome P450 BM-3 complexed with N-palmitoylglycine: a replica exchange molecular dynamics study.

Emilio Gallicchio, R. Friesner, R. Levy, 2006, Journal of the American Chemical Society.

Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network

R. Levy, A. Olson, W. Flynn, 2019, J. Chem. Inf. Model..

Improving Prediction Accuracy of Binding Free Energies and Poses of HIV Integrase Complexes Using the Binding Energy Distribution Analysis Method with Flattening Potentials

R. Levy, W. Flynn, J. Xia, 2018, J. Chem. Inf. Model..

Cavity Particle in Aqueous Solution with a Hydrophobic Solute: Structure, Energetics, and Functionals.

Bin W. Zhang, R. Levy, N. Matubayasi, 2020, The journal of physical chemistry. B.

Correlation between 13Cα chemical shifts and helix content of peptide ensembles

R. Levy, J. Baum, Daniel S. Weinstock, 2008, Protein science : a publication of the Protein Society.

THE EFFECT OF ADDED ELECTROLYTE ON HYDROGEN-BONDING EQUILIBRIUM IN DILUTE SOLUTIONS OF t-BUTYL ALCOHOL IN CARBON TETRACHLORIDE

R. Levy, J. Hyne, 1962 .

Molecular dynamics of an alpha-helical polypeptide: Temperature dependence and deviation from harmonic behavior.

M Karplus, M. Karplus, R. Levy, 1982, Proceedings of the National Academy of Sciences of the United States of America.

Mi3-GPU: MCMC-based inverse Ising inference on GPUs for protein covariation analysis

Ronald M. Levy, Allan Haldane, R. Levy, 2020, Comput. Phys. Commun..

Long-time conformational transitions of alanine dipeptide in aqueous solution: Continuous and discrete-state kinetic models

Ronald M. Levy, R. Levy, D. Chekmarev, 2004 .

Tertiary contacts in alpha-lactalbumin at pH 7 and pH 2: a molecular dynamics study.

R. Levy, J. Baum, N. Li, 1998, Journal of biomolecular structure & dynamics.

In silico vaccine design based on molecular simulations of rhinovirus chimeras presenting HIV-1 gp41 epitopes.

R. Levy, E. Arnold, G. F. Arnold, 2009, Journal of molecular biology.

A framework for flexible and scalable replica-exchange on production distributed CI

Wei Dai, Shantenu Jha, Melissa Romanus, 2013, XSEDE.

Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations.

Emilio Gallicchio, Ronald M Levy, R. Levy, 2012, Journal of chemical theory and computation.