Ronald M. Levy

Ronald M. Levy's AcademicInfluence.com Rankings

Ronald M. Levy

Biology

#12690

World Rank

#16183

Historical Rank

#2652

USA Rank

Biochemistry

#2182

World Rank

#2327

Historical Rank

#305

USA Rank

biology Degrees

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Biology

Ronald M. Levy's Degrees

PhD Biochemistry University of California, Berkeley
Bachelors Chemistry University of California, Berkeley

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Ronald M. Levy's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

Integrated Modeling Program, Applied Chemical Theory (IMPACT) (2005) (1093)
AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high‐resolution modeling (2004) (299)
Structural Organization of Bacterial RNA Polymerase Holoenzyme and the RNA Polymerase-Promoter Open Complex (2002) (294)
Enthalpy−Entropy and Cavity Decomposition of Alkane Hydration Free Energies: Numerical Results and Implications for Theories of Hydrophobic Solvation (2000) (250)
Simplified amino acid alphabets for protein fold recognition and implications for folding. (2000) (235)
On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy. (2003) (235)
Evaluation of the configurational entropy for proteins: application to molecular dynamics simulations of an α-helix (1984) (213)
Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects. (1998) (208)
Quasi‐harmonic method for studying very low frequency modes in proteins (1984) (208)
The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators (2002) (198)
Antibacterial peptide microcin J25 inhibits transcription by binding within and obstructing the RNA polymerase secondary channel. (2004) (195)
Computer simulations of the dielectric properties of water: Studies of the simple point charge and transferrable intermolecular potential models (1989) (170)
An Anisotropic Polarizable Water Model: Incorporation of All-Atom Polarizabilities into Molecular Mechanics Force Fields (1994) (167)
Temperature weighted histogram analysis method, replica exchange, and transition paths. (2005) (158)
Effect of anisotropy and anharmonicity on protein crystallographic refinement. An evaluation by molecular dynamics. (1986) (156)
Structural reorganization of alpha-synuclein at low pH observed by NMR and REMD simulations. (2009) (156)
Gaussian fluctuation formula for electrostatic free‐energy changes in solution (1991) (138)
On finite‐size effects in computer simulations using the Ewald potential (1995) (137)
The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities. (2010) (130)
Molecular dynamics simulation of solvated protein at high pressure. (1992) (128)
Theory of binless multi-state free energy estimation with applications to protein-ligand binding. (2012) (125)
Conformational Analysis of the DFG-Out Kinase Motif and Biochemical Profiling of Structurally Validated Type II Inhibitors (2014) (125)
Comparative Performance of Several Flexible Docking Programs and Scoring Functions: Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets (2007) (123)
HIV-1 reverse transcriptase structure with RNase H inhibitor dihydroxy benzoyl naphthyl hydrazone bound at a novel site. (2006) (123)
Protein folding pathways from replica exchange simulations and a kinetic network model. (2005) (122)
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 (2002) (119)
A large data set comparison of protein structures determined by crystallography and NMR: Statistical test for structural differences and the effect of crystal packing (2007) (117)
New Linear Interaction Method for Binding Affinity Calculations Using a Continuum Solvent Model (2001) (117)
Direct Determination of Kinetic Rates from Single-Molecule Photon Arrival Trajectories Using Hidden Markov Models. (2003) (117)
Diffusive langevin dynamics of model alkanes (1979) (111)
Motional averaging of proton nuclear Overhauser effects in proteins. Predictions from a molecular dynamics simulation of lysozyme (1984) (108)
Solvent models for protein–ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations (2001) (107)
Entropy−Enthalpy Compensation in Solvation and Ligand Binding Revisited (1998) (107)
The AGBNP2 Implicit Solvation Model. (2009) (106)
Large scale simulation of macromolecules in solution: Combining the periodic fast multipole method with multiple time step integrators (1997) (104)
Recent theoretical and computational advances for modeling protein-ligand binding affinities. (2011) (103)
alpha-Helix dipole model and electrostatic stabilization of 4-alpha-helical proteins. (1982) (102)
Free energy surfaces of β‐hairpin and α‐helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model (2004) (100)
Helix–coil transitions in a simple polypeptide model (1980) (97)
Solvent effects on optical absorption spectra: the 1A1 .fwdarw. 1A2 transition of formaldehyde in water (1989) (96)
Inference of signaling and gene regulatory networks by steady-state perturbation experiments: structure and accuracy. (2005) (94)
Protein dynamics and NMR relaxation: comparison of simulations with experiment (1982) (91)
Simulating replica exchange simulations of protein folding with a kinetic network model (2007) (89)
Advances in all atom sampling methods for modeling protein-ligand binding affinities. (2011) (89)
NMR relaxation parameters in molecules with internal motion: exact Langevin trajectory results compared with simplified relaxation models (1981) (89)
Molecular dynamics of an alpha-helical polypeptide: Temperature dependence and deviation from harmonic behavior. (1982) (89)
Vibrational approach to the dynamics of an α‐helix (1979) (84)
Thermodynamics of the Hydration Shell. 1. Excess Energy of a Hydrophobic Solute (1994) (83)
Thermodynamics of the Hydration Shell. 2. Excess Volume and Compressibility of a Hydrophobic Solute (1996) (81)
Protein hydration and unfolding--insights from experimental partial specific volumes and unfolded protein models. (1998) (80)
Molecular dynamics simulation of time-resolved fluorescence and nonequilibrium solvation of formaldehyde in water (1990) (79)
On Finite-Size Corrections to the Free Energy of Ionic Hydration (1997) (78)
Long-time conformational transitions of alanine dipeptide in aqueous solution: Continuous and discrete-state kinetic models (2004) (75)
Conserving energy during molecular dynamics simulations of water, proteins, and proteins in water (1990) (75)
Intrinsic pKas of ionizable residues in proteins: An explicit solvent calculation for lysozyme (1994) (74)
Molecular dynamics simulations of water with Ewald summation for the long range electrostatic interactions (1991) (74)
Vibrational relaxation and Bloch–Redfield theory (1992) (72)
Protein backbone structure determination using only residual dipolar couplings from one ordering medium (2001) (72)
A Model for Studying Drying at Hydrophobic Interfaces: Structural and Thermodynamic Properties† (2001) (71)
SOLVATION FREE ENERGIES OF SMALL AMIDES AND AMINES FROM MOLECULAR DYNAMICS/FREE ENERGY PERTURBATION SIMULATIONS USING PAIRWISE ADDITIVE AND MANY-BODY POLARIZABLE POTENTIALS (1995) (71)
Conformational equilibria and free energy profiles for the allosteric transition of the ribose-binding protein. (2005) (68)
Large scale affinity calculations of cyclodextrin host-guest complexes: Understanding the role of reorganization in the molecular recognition process. (2013) (67)
Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling. (2008) (64)
Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update. (2003) (64)
Monte Carlo Study of the Effect of Pressure on Hydrophobic Association (1997) (58)
Potts Hamiltonian models of protein co-variation, free energy landscapes, and evolutionary fitness. (2017) (57)
Molecular dynamics of myoglobin at 298 degrees K. Results from a 300-ps computer simulation. (1985) (57)
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. (1990) (57)
Dielectric and thermodynamic response of a generalized reaction field model for liquid state simulations (1993) (56)
Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases (2000) (55)
Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations. (2012) (55)
Quasi-harmonic method for calculating vibrational spectra from classical simulations on multi-dimensional anharmonic potential surfaces (1984) (53)
Distinguishing Binders from False Positives by Free Energy Calculations: Fragment Screening Against the Flap Site of HIV Protease (2014) (53)
Viewing the born model for ion hydration through a microscope (1988) (52)
Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations. (2011) (52)
Conformational equilibrium of cytochrome P450 BM-3 complexed with N-palmitoylglycine: a replica exchange molecular dynamics study. (2006) (51)
Ca2+ dependence of tension and ADP production in segments of chemically skinned muscle fibers. (1976) (50)
Increase of carbon-13 NMR relaxation times in proteins due to picosecond motional averaging (1981) (50)
Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge (2014) (50)
How kinetics within the unfolded state affects protein folding: an analysis based on markov state models and an ultra-long MD trajectory. (2013) (50)
Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM) (2012) (49)
Estimation of dynamic parameters from NMR relaxation data using the Lipari-Szabo model-free approach and Bayesian statistical methods. (1999) (47)
Structural propensities of kinase family proteins from a Potts model of residue co‐variation (2016) (47)
Thermodynamic Decomposition of Hydration Free Energies by Computer Simulation: Application to Amines, Oxides, and Sulfides (1997) (46)
Inference of Epistatic Effects Leading to Entrenchment and Drug Resistance in HIV-1 Protease (2016) (46)
Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations. (2011) (45)
An optimized harmonic reference system for the evaluation of discretized path integrals (1984) (45)
Solution structures of proteins from NMR data and modeling: alternative folds for neutrophil peptide 5. (1989) (44)
In silico vaccine design based on molecular simulations of rhinovirus chimeras presenting HIV-1 gp41 epitopes. (2009) (44)
Asynchronous replica exchange for molecular simulations (2008) (43)
Field strength dependence of dielectric saturation in liquid water (1990) (42)
Crankshaft motions of the polypeptide backbone in molecular dynamics simulations of human type-α transforming growth factor (1995) (42)
Distance-restrained docking of rifampicin and rifamycin SV to RNA polymerase using systematic FRET measurements: developing benchmarks of model quality and reliability. (2005) (40)
Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model. (2004) (39)
Global folding of proteins using a limited number of distance constraints. (1993) (39)
The mechanism of H171T resistance reveals the importance of Nδ-protonated His171 for the binding of allosteric inhibitor BI-D to HIV-1 integrase (2014) (38)
Linear Interaction Energy (LIE) Models for Ligand Binding in Implicit Solvent: Theory and Application to the Binding of NNRTIs to HIV-1 Reverse Transcriptase. (2007) (38)
Initial fluorescence depolarization of tyrosines in proteins (1982) (38)
On the local and nonlocal components of solvation thermodynamics and their relation to solvation shell models (1998) (36)
Motions of an α‐helical polypeptide: Comparison of molecular and harmonic dynamics (1990) (36)
PrimeX and the Schrödinger computational chemistry suite of programs (2012) (36)
Propagation of experimental uncertainties using the Lipari-Szabo model-free analysis of protein dynamics (1998) (36)
Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease (2009) (35)
Identification of Alternative Binding Sites for Inhibitors of HIV-1 Ribonuclease H Through Comparative Analysis of Virtual Enrichment Studies (2011) (35)
Deep Sequencing of Protease Inhibitor Resistant HIV Patient Isolates Reveals Patterns of Correlated Mutations in Gag and Protease (2015) (34)
Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit. (2016) (34)
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. (2009) (34)
Simple continuous and discrete models for simulating replica exchange simulations of protein folding. (2008) (34)
Correlated Electrostatic Mutations Provide a Reservoir of Stability in HIV Protease (2012) (32)
Comparative Performance of Several Flexible Docking Programs and Scoring Functions: Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets. (2007) (32)
Corrections to the quasiharmonic approximation for evaluating molecular entropies (1986) (32)
Asynchronous replica exchange software for grid and heterogeneous computing (2015) (32)
HIV-1 integrase tetramers are the antiviral target of pyridine-based allosteric integrase inhibitors (2019) (31)
Allosteric HIV‐1 integrase inhibitors promote aberrant protein multimerization by directly mediating inter‐subunit interactions: Structural and thermodynamic modeling studies (2016) (31)
Determination of Protein Structures in Solution Using Nmr Data and Impact (1988) (30)
Investigation of the Polymeric Properties of α-Synuclein and Comparison with NMR Experiments: A Replica Exchange Molecular Dynamics Study. (2012) (30)
Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction (2004) (30)
Structural Reorganization of α-Synuclein at Low pH Observed by NMR and REMD Simulations (2009) (29)
Protein structural motif recognition via NMR residual dipolar couplings. (2001) (28)
A Stochastic Solution to the Unbinned WHAM Equations. (2015) (27)
NMR relaxation in proteins with fast internal motions and slow conformational exchange: model-free framework and Markov state simulations. (2013) (27)
Ionic association in methanol and related solvents: an extended RISM analysis (1987) (26)
The linear interaction energy method for the prediction of protein stability changes upon mutation (2012) (26)
Simple models for solvation effects on electronic transition energies: Formaldehyde and water (1989) (26)
Recovering kinetics from a simplified protein folding model using replica exchange simulations: a kinetic network and effective stochastic dynamics. (2009) (25)
Molecular dynamics of an a-helical polypeptide: Temperature dependence and deviation from harmonic behavior (protein dynamics/temperature factor/quantum corrections/fluctuations/normal modes) (1982) (24)
Temperature-dependent molecular dynamics and restrained X-ray refinement simulations of a Z-DNA hexamer. (1986) (24)
A molecular dynamics study of pressure effects on solvation and optical spectra : the ground and excited states of formaldehyde in water (1991) (24)
Comparing alchemical and physical pathway methods for computing the absolute binding free energy of charged ligands. (2018) (23)
Dipolar NMR relaxation of nonprotonated aromatic carbons in proteins. Structural and dynamical effects. (1982) (23)
Salt-induced conformational changes in DNA: analysis using the polymer RISM theory (1989) (23)
Distinguishing among structural ensembles of the GB1 peptide: REMD simulations and NMR experiments. (2007) (22)
Variable quadratic propagator for quantum Monte Carlo simulations (1988) (22)
Prediction of pKa Shifts without Truncation of Electrostatic Interactions: An Explicit Solvent Calculation for Succinic Acid (1996) (22)
The Role of Interfacial Water in Protein-Ligand Binding: Insights from the Indirect Solvent Mediated Potential of Mean Force. (2018) (21)
a-Helix dipole model and electrostatic stabilization of 4-a-helical proteins (21)
How long does it take to equilibrate the unfolded state of a protein? (2013) (21)
A New Class of Allosteric HIV-1 Integrase Inhibitors Identified by Crystallographic Fragment Screening of the Catalytic Core Domain* (2016) (20)
Molecular Dynamics of the Proline Switch and Its Role in Crk Signaling (2014) (20)
BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge (2015) (20)
Conformational dynamics of substrate in the active site of cytochrome P450 BM-3/NPG complex: insights from NMR order parameters. (2007) (20)
Dielectric response of solvent surrounding an ion pair: Ewald potential versus spherical truncation (1996) (20)
Parameterization of an effective potential for protein–ligand binding from host–guest affinity data (2016) (19)
A combined treatment of hydration and dynamical effects for the modeling of host–guest binding thermodynamics: the SAMPL5 blinded challenge (2016) (19)
Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation. (2016) (19)
The transition between active and inactive conformations of Abl kinase studied by rock climbing and Milestoning. (2019) (19)
Conformational populations of ligand‐sized molecules by replica exchange molecular dynamics and temperature reweighting (2009) (19)
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. (2009) (19)
Protein sequential resonance assignments by combinatorial enumeration using 13Cα chemical shifts and their (i, i−1) sequential connectivities (2002) (18)
Correlated helix–coil transitions in polypeptides (1981) (18)
Large‐scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis (2015) (18)
Epistasis and entrenchment of drug resistance in HIV-1 subtype B (2019) (18)
Coevolutionary Landscape of Kinase Family Proteins: Sequence Probabilities and Functional Motifs. (2018) (18)
Molecular mechanics and electrostatic effects. (1994) (18)
The generative capacity of probabilistic protein sequence models (2020) (17)
Large scale free energy calculations for blind predictions of protein–ligand binding: the D3R Grand Challenge 2015 (2016) (17)
Chloride Ion Hydration and Diffusion in Supercritical Water Using a Polarizable Water Model (2002) (17)
A new RISM integral equation for solvated polymers (1987) (17)
Three-dimensional structure of echistatin and dynamics of the active site (1994) (17)
Chimeric Rhinoviruses Displaying MPER Epitopes Elicit Anti-HIV Neutralizing Responses (2013) (15)
Impact of the Precision in NMR Relaxation Measurements on the Interpretation of Protein Dynamics (1997) (15)
Influence of multiple-sequence-alignment depth on Potts statistical models of protein covariation. (2018) (14)
A Bayesian statistical method for the detection and quantification of rotational diffusion anisotropy from NMR relaxation data. (2000) (14)
Combined effect of restricted rotational diffusion plus jumps on nuclear magnetic resonance and fluorescence probes of aromatic ring motions in proteins. (1983) (13)
Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular Dynamics Applications (2006) (13)
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 (2017) (13)
Molecular electrostatic potentials and partial atomic charges from correlated wave functions: Applications to the electronic ground and excited states of 3‐methylindole (1992) (13)
Stabilization of α-helical secondary structure during high-temperature molecular-dynamics simulations of α-lactalbumin (1991) (13)
Estimation of interatomic distances in proteins from NOE spectra at longer mixing times using an empirical two-spin equation (1993) (13)
Solvent effects on the adiabatic free energy difference between the ground and excited states of methylindole in water (1991) (13)
Functional Group Contributions to Partial Molar Compressibilities of Alcohols in Water (2000) (12)
Mi3-GPU: MCMC-based inverse Ising inference on GPUs for protein covariation analysis (2020) (12)
Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling. (2008) (12)
The UWHAM and SWHAM Software Package (2019) (12)
Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses (2020) (11)
Molecular mechanics parameters for electronically excited states: The (n, π*) singlet state of formaldehyde (1990) (11)
Antigenic characteristics of rhinovirus chimeras designed in silico for enhanced presentation of HIV-1 gp41 epitopes [corrected]. (2010) (11)
Solvent effects on the torsional dynamics of a twisted intramolecular charge transfer (TICT) molecule: bianthryl in acetonitrile (1993) (11)
Computer Simulations of Macromolecular Dynamics: Models for Vibrational Spectroscopy and X‐Ray Refinement a (1986) (10)
The mechanism of H 171 T resistance reveals the importance of N δ-protonated His 171 for the binding of allosteric inhibitor BID to HIV-1 integrase (2014) (10)
Relationship between Solvation Thermodynamics from IST and DFT Perspectives. (2017) (10)
Spatially-Decomposed Free Energy of Solvation Based on the Endpoint Density-Functional Method. (2019) (10)
Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation. (2016) (10)
Exploring the Free-Energy Landscape and Thermodynamics of Protein-Protein Association. (2020) (9)
Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies. (2015) (9)
Molecular dynamics studies of NMR relaxation in proteins. (1980) (9)
Correlation between 13Cα chemical shifts and helix content of peptide ensembles (2008) (9)
THE EFFECT OF ADDED ELECTROLYTE ON HYDROGEN-BONDING EQUILIBRIUM IN DILUTE SOLUTIONS OF t-BUTYL ALCOHOL IN CARBON TETRACHLORIDE (1962) (9)
Analysis of side‐chain conformational distributions in neutrophil peptide‐5 nmr structures (1990) (9)
First Passage Times, Lifetimes, and Relaxation Times of Unfolded Proteins. (2015) (9)
Large‐Scale Asynchronous and Distributed Multidimensional Replica Exchange Molecular Simulations and Efficiency Analysis (2016) (9)
Molecular Dynamics Free Energy Simulations Reveal the Mechanism for the Antiviral Resistance of the M66I HIV-1 Capsid Mutation (2021) (8)
A framework for flexible and scalable replica-exchange on production distributed CI (2013) (8)
The Excess Chemical Potential of Water at the Interface with a Protein from End Point Simulations. (2018) (8)
Stratified UWHAM and Its Stochastic Approximation for Multicanonical Simulations Which Are Far from Equilibrium. (2017) (8)
A relaxation-matrix analysis of distance-constraint ranges for NOEs in proteins at long mixing times. (1995) (8)
Improving Prediction Accuracy of Binding Free Energies and Poses of HIV Integrase Complexes Using the Binding Energy Distribution Analysis Method with Flattening Potentials (2018) (7)
Solvent Effects on Optical Absorption Spectra: The 1A1 → 1A2 Transition of Formaldehyde in Water. (1989) (7)
Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates. (2018) (7)
Implementation of a macromolecular mechanics program on a cyber 205 supercomputer (1986) (7)
Visualization of energetics and conformations from molecular computer simulations (1986) (6)
Normal mode paths for hydrogen exchange in the peptide ferrichrome. (1983) (6)
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)] (1997) (6)
Simulating the effect of the two-spin approximation on the generation of protein structures from NOE data (1992) (6)
Correction: Chimeric Rhinoviruses Displaying MPER Epitopes Elicit Anti-HIV Neutralizing Responses (2013) (6)
Trajectory Studies of NMR Relaxation in Flexible Molecules (1983) (6)
Implicit solvent models for protein-ligand binding: Insights based on explicit solvent simulations (1999) (6)
Evaluating polarizable potentials on distributed memory parallel computers: Program development and applications (1995) (5)
Computational design of small molecular modulators of protein–protein interactions with a novel thermodynamic cycle: Allosteric inhibitors of HIV‐1 integrase (2020) (5)
Computer simulations of protein dynamics: theory and experiment (1986) (4)
Induction of contractile activity by rigor complexes in myofibrils. (1977) (4)
Detecting Native Protein Folds among Large Decoy Sets with the OPLS All‐Atom Potential and the Surface Generalized Born Solvent Model (2002) (4)
Tertiary contacts in alpha-lactalbumin at pH 7 and pH 2: a molecular dynamics study. (1998) (3)
Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network (2019) (3)
Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid (2022) (3)
Antigenic Characteristics of Rhinovirus Chimeras Designed in silico for En 5 hanced Presentation of HIV-1 gp 41 Epitopes (2010) (3)
Ligand Binding Thermodynamic Cycles: Hysteresis, LWHAM, and the Overlapping States Matrix. (2019) (2)
Exploring the Free Energy Landscape and Thermodynamics of Protein-Protein Association: HIV-1 Integrase Multimerization Induced by an Allosteric Inhibitor (2020) (2)
Ligand Binding Thermodynamic Cycles: Hysteresis, the Locally Weighted Histogram Analysis Method, and the Overlapping States Matrix (2019) (2)
Protein Folding and Binding: Effective Potentials, Replica Exchange Simulations, and Network Models (2009) (2)
Simulation of photophysical processes of indoles in solution (1992) (2)
Using Macromolecular Dynamics Simulations to Interpret Experiments (1986) (2)
Unique Features of Different Classes of G-Protein-Coupled Receptors Revealed from Sequence Coevolutionary and Structural Analysis (2021) (2)
Biomolecular processes: dynamics of proteins and nucleic acids. (1988) (2)
The role of epistasis in determining the fitness landscape of HIV proteins (2021) (1)
Insights into the energy landscapes of chromosome organization proteins from coevolutionary sequence variation and structural modeling (2020) (1)
Cavity Particle in Aqueous Solution with a Hydrophobic Solute: Structure, Energetics, and Functionals. (2020) (1)
X-ray structure for an RNase H inhibitor bound to HIV-1 reverse transcriptase (2005) (1)
Solvation Thermodynamics from the Perspective of Endpoints DFT. (2020) (1)
Author response: Epistasis and entrenchment of drug resistance in HIV-1 subtype B (2019) (1)
Protein Loop Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates. (2021) (1)
Molecular Dynamics Simulation of Solvated Protein at High Pressuret (2001) (0)
Motions of an Molecular and a-Helical Polypeptide : Harmonic Dynamics Comparison of (2009) (0)
Crystal structure of HIV-1 reverse transcriptase (RT) in complex with DHBNH, an RNASE H inhibitor (2006) (0)
Protein Kinase Free Energy Landscapes: The Role of the Activation Loop (2019) (0)
Recollection (2016) (0)
The mechanism of H171T resistance reveals the importance of Nδ-protonated His171 for the binding of allosteric inhibitor BI-D to HIV-1 integrase (2014) (0)
Coevolutionary Landscapes of Kinase Family Proteins (2019) (0)
The Rutgers Computational Grid: A Distributed Linux PC Cluster (2003) (0)
The generative capacity of probabilistic protein sequence models (2021) (0)
CRYSTALLOGRAPHY OF BIOLOGICAL MACROMOLECULES C246 (2005) (0)
Crystal structure of the Actinomadura R39 DD-peptidase (PBP4) (2005) (0)
HIV-1 Integrase Tetramers are the Antiviral Target of Pyridine-based Allosteric Integrase 1 Inhibitors 2 3 (0)
Trajectory Studies of in Flexible Molecules NMR Relaxation (2009) (0)
Shallow Free Energy Landscapes Remodelled by Ligand Binding (2007) (0)
Fold Recognition using the OPLS All-Atom Potential and the Surface Generalized Born Solvent Model (2002) (0)
Temporal Evolution of the HIV Viral Population under Drug Selection Pressure (2022) (0)
17 M ar 2 00 9 The AGBNP 2 Implicit Solvation Model (2009) (0)
Erratum to “Antigenic Characteristics of Rhinovirus Chimeras Designed in silico for Enhanced Presentation of HIV-1 gp41 Epitopes” [J. Mol. Biol. 397 (2010) 752–766] (2010) (0)
Contingency and Entrenchment of Drug-Resistance Mutations in HIV Viral Proteins. (2022) (0)
Biophysical Chemistry Molecular mechanics and electrostatic effects (2009) (0)
DIFFUSIVE DYNAMICS OF ALKANE CHAINS (2009) (0)
Erratum to: A combined treatment of hydration and dynamical effects for the modeling of host–guest binding thermodynamics: the SAMPL5 blinded challenge (2016) (0)
Mechanisms of HIV-1 Integrase Resistance to Dolutegravir and Potent Inhibition of Drug Resistant Variants (2023) (0)
MOLECULAR DYNAMICS OF MYOGLOBIN AT 2980K Results from a 300-ps Computer Simulation (2005) (0)
Exploring the Kinetics and Folding Pathways of Trp-cage using a Kinetic Network Model (2010) (0)
Using Computer Simulations To Probe the Structure and Dynamics of Biopolymers (1987) (0)
The Rutgers Computational Grid Based on Linux PC Cluster (2001) (0)
EvaluaLing Polarizable Potentials on Distributed Memory Parallel Computers : Program Development and Applications (2009) (0)
A 61 , C 249 X-ray Structure for an RNase H Inhibitor Bound to HIV-1 Reverse Transcriptase (2005) (0)
Evolutionary divergence in the conformational landscapes of tyrosine vs serine/threonine kinases (2022) (0)

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What Schools Are Affiliated With Ronald M. Levy?

Ronald M. Levy is affiliated with the following schools:

University of California, Berkeley
Reed College
Rutgers University
University of Pittsburgh
Columbia University
Temple University
Kyoto University
Harvard University