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Top Articles

#TitleJournalYearCitations
1Potts Hamiltonian models of protein co-variation, free energy landscapes, and evolutionary fitnessCurrent Opinion in Structural Biology201773
2Inference of Epistatic Effects Leading to Entrenchment and Drug Resistance in HIV-1 ProteaseMolecular Biology and Evolution201751
3Structural propensities of kinase family proteins from a Potts model of residue co‐variationProtein Science201650
4Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping LimitJournal of Physical Chemistry B201642
5Deep Sequencing of Protease Inhibitor Resistant HIV Patient Isolates Reveals Patterns of Correlated Mutations in Gag and ProteasePLoS Computational Biology201538
6Asynchronous replica exchange software for grid and heterogeneous computingComputer Physics Communications201535
7Comparing alchemical and physical pathway methods for computing the absolute binding free energy of charged ligandsPhysical Chemistry Chemical Physics201834
8The generative capacity of probabilistic protein sequence modelsNature Communications202128
9A Stochastic Solution to the Unbinned WHAM EquationsJournal of Physical Chemistry Letters201527
10The Role of Interfacial Water in Protein–Ligand Binding: Insights from the Indirect Solvent Mediated Potential of Mean ForceJournal of Chemical Theory and Computation201825
11Epistasis and entrenchment of drug resistance in HIV-1 subtype BELife201925
12A New Class of Allosteric HIV-1 Integrase Inhibitors Identified by Crystallographic Fragment Screening of the Catalytic Core DomainJournal of Biological Chemistry201620
13Large‐scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysisJournal of Computational Chemistry201519
14Coevolutionary Landscape of Kinase Family Proteins: Sequence Probabilities and Functional MotifsBiophysical Journal201819
15A combined treatment of hydration and dynamical effects for the modeling of host–guest binding thermodynamics: the SAMPL5 blinded challengeJournal of Computer-Aided Molecular Design201718
16BEDAM binding free energy predictions for the SAMPL4 octa-acid host challengeJournal of Computer-Aided Molecular Design201517
17Influence of multiple-sequence-alignment depth on Potts statistical models of protein covariationPhysical Review E201917
18Mi3-GPU: MCMC-based inverse Ising inference on GPUs for protein covariation analysisComputer Physics Communications202117
19Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimationJournal of Chemical Physics201616
20Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the PosesJournal of Computational Chemistry202016
21Relationship between Solvation Thermodynamics from IST and DFT PerspectivesJournal of Physical Chemistry B201714
22Spatially-Decomposed Free Energy of Solvation Based on the Endpoint Density-Functional MethodJournal of Chemical Theory and Computation201912
23Conformational Free Energy Changes via an Alchemical Path without Reaction CoordinatesJournal of Physical Chemistry Letters201811
24The Excess Chemical Potential of Water at the Interface with a Protein from End Point SimulationsJournal of Physical Chemistry B201810
25Stratified UWHAM and Its Stochastic Approximation for Multicanonical Simulations Which Are Far from EquilibriumJournal of Chemical Theory and Computation20179
26The UWHAM and SWHAM Software PackageScientific Reports20199
27Molecular Dynamics Simulation and Analysis of the Antimicrobial Peptide–Lipid Bilayer InteractionsMethods in Molecular Biology20178
28Ligand Binding Thermodynamic Cycles: Hysteresis, the Locally Weighted Histogram Analysis Method, and the Overlapping States MatrixJournal of Chemical Theory and Computation20208
29Improving Prediction Accuracy of Binding Free Energies and Poses of HIV Integrase Complexes Using the Binding Energy Distribution Analysis Method with Flattening PotentialsJournal of Chemical Information and Modeling20187
30Evolutionary divergence in the conformational landscapes of tyrosine vs serine/threonine kinasesELife07
31Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed NetworkJournal of Chemical Information and Modeling20196
32Limits to detecting epistasis in the fitness landscape of HIVPLoS ONE20226
33Unique features of different classes of G‐protein‐coupled receptors revealed from sequence coevolutionary and structural analysisProteins: Structure, Function and Bioinformatics20224
34Contingency and Entrenchment of Drug-Resistance Mutations in HIV Viral ProteinsJournal of Physical Chemistry B20224
35Cavity Particle in Aqueous Solution with a Hydrophobic Solute: Structure, Energetics, and FunctionalsJournal of Physical Chemistry B20201
36RecollectionProtein Science20160
37Insights into the energy landscapes of chromosome organization proteins from coevolutionary sequence variation and structural modelingProceedings of the National Academy of Sciences of the United States of America20200