# | Title | Journal | Year | Citations |
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1 | Potts Hamiltonian models of protein co-variation, free energy landscapes, and evolutionary fitness | Current Opinion in Structural Biology | 2017 | 73 |
2 | Inference of Epistatic Effects Leading to Entrenchment and Drug Resistance in HIV-1 Protease | Molecular Biology and Evolution | 2017 | 51 |
3 | Structural propensities of kinase family proteins from a Potts model of residue co‐variation | Protein Science | 2016 | 50 |
4 | Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit | Journal of Physical Chemistry B | 2016 | 42 |
5 | Deep Sequencing of Protease Inhibitor Resistant HIV Patient Isolates Reveals Patterns of Correlated Mutations in Gag and Protease | PLoS Computational Biology | 2015 | 38 |
6 | Asynchronous replica exchange software for grid and heterogeneous computing | Computer Physics Communications | 2015 | 35 |
7 | Comparing alchemical and physical pathway methods for computing the absolute binding free energy of charged ligands | Physical Chemistry Chemical Physics | 2018 | 34 |
8 | The generative capacity of probabilistic protein sequence models | Nature Communications | 2021 | 28 |
9 | A Stochastic Solution to the Unbinned WHAM Equations | Journal of Physical Chemistry Letters | 2015 | 27 |
10 | The Role of Interfacial Water in Protein–Ligand Binding: Insights from the Indirect Solvent Mediated Potential of Mean Force | Journal of Chemical Theory and Computation | 2018 | 25 |
11 | Epistasis and entrenchment of drug resistance in HIV-1 subtype B | ELife | 2019 | 25 |
12 | A New Class of Allosteric HIV-1 Integrase Inhibitors Identified by Crystallographic Fragment Screening of the Catalytic Core Domain | Journal of Biological Chemistry | 2016 | 20 |
13 | Large‐scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis | Journal of Computational Chemistry | 2015 | 19 |
14 | Coevolutionary Landscape of Kinase Family Proteins: Sequence Probabilities and Functional Motifs | Biophysical Journal | 2018 | 19 |
15 | A combined treatment of hydration and dynamical effects for the modeling of host–guest binding thermodynamics: the SAMPL5 blinded challenge | Journal of Computer-Aided Molecular Design | 2017 | 18 |
16 | BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge | Journal of Computer-Aided Molecular Design | 2015 | 17 |
17 | Influence of multiple-sequence-alignment depth on Potts statistical models of protein covariation | Physical Review E | 2019 | 17 |
18 | Mi3-GPU: MCMC-based inverse Ising inference on GPUs for protein covariation analysis | Computer Physics Communications | 2021 | 17 |
19 | Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation | Journal of Chemical Physics | 2016 | 16 |
20 | Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses | Journal of Computational Chemistry | 2020 | 16 |
21 | Relationship between Solvation Thermodynamics from IST and DFT Perspectives | Journal of Physical Chemistry B | 2017 | 14 |
22 | Spatially-Decomposed Free Energy of Solvation Based on the Endpoint Density-Functional Method | Journal of Chemical Theory and Computation | 2019 | 12 |
23 | Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates | Journal of Physical Chemistry Letters | 2018 | 11 |
24 | The Excess Chemical Potential of Water at the Interface with a Protein from End Point Simulations | Journal of Physical Chemistry B | 2018 | 10 |
25 | Stratified UWHAM and Its Stochastic Approximation for Multicanonical Simulations Which Are Far from Equilibrium | Journal of Chemical Theory and Computation | 2017 | 9 |
26 | The UWHAM and SWHAM Software Package | Scientific Reports | 2019 | 9 |
27 | Molecular Dynamics Simulation and Analysis of the Antimicrobial Peptide–Lipid Bilayer Interactions | Methods in Molecular Biology | 2017 | 8 |
28 | Ligand Binding Thermodynamic Cycles: Hysteresis, the Locally Weighted Histogram Analysis Method, and the Overlapping States Matrix | Journal of Chemical Theory and Computation | 2020 | 8 |
29 | Improving Prediction Accuracy of Binding Free Energies and Poses of HIV Integrase Complexes Using the Binding Energy Distribution Analysis Method with Flattening Potentials | Journal of Chemical Information and Modeling | 2018 | 7 |
30 | Evolutionary divergence in the conformational landscapes of tyrosine vs serine/threonine kinases | ELife | 0 | 7 |
31 | Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network | Journal of Chemical Information and Modeling | 2019 | 6 |
32 | Limits to detecting epistasis in the fitness landscape of HIV | PLoS ONE | 2022 | 6 |
33 | Unique features of different classes of G‐protein‐coupled receptors revealed from sequence coevolutionary and structural analysis | Proteins: Structure, Function and Bioinformatics | 2022 | 4 |
34 | Contingency and Entrenchment of Drug-Resistance Mutations in HIV Viral Proteins | Journal of Physical Chemistry B | 2022 | 4 |
35 | Cavity Particle in Aqueous Solution with a Hydrophobic Solute: Structure, Energetics, and Functionals | Journal of Physical Chemistry B | 2020 | 1 |
36 | Recollection | Protein Science | 2016 | 0 |
37 | Insights into the energy landscapes of chromosome organization proteins from coevolutionary sequence variation and structural modeling | Proceedings of the National Academy of Sciences of the United States of America | 2020 | 0 |