Publications
] .
2023. Molecular determinants of inhibition of UCP1-mediated respiratory uncoupling.. Nat Commun. 14(1):2594.
.
2022. Consistent Picture of Phosphate–Divalent Cation Binding from Models with Implicit and Explicit Electronic Polarization. J. Phys. Chem. B. 126(22):4022-4034.
.
2022. Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0]. Living Journal of Computational Molecular Science. 4:1583.
.
2022. Human Learning for Molecular Simulations: The Collective Variables Dashboard in VMD.. J Chem Theory Comput. 18(3):1945-1956.
.
2022. Multiscale Computational Study of the Conformation of the Full-Length Intrinsically Disordered Protein MeCP2.. J Chem Inf Model. 62(4):958-970.
.
2022. Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation. Nature Communications. 13
.
2022. Symmetry-Adapted Restraints for Binding Free Energy Calculations.. J Chem Theory Comput.
.
2021. Building intuition for binding free energy calculations: Bound state definition, restraints, and symmetry. The Journal of Chemical Physics. 154:204101.
.
2021. Fast and Accurate Multidimensional Free Energy Integration.. J Chem Theory Comput. 17(11):6789-6798.
.
2021. Mechanistic Insights on Heme-to-Heme Transmembrane Electron Transfer Within NADPH Oxydases From Atomistic Simulations.. Front Chem. 9:650651.
.
2020. Binding of divalent cations to acetate: molecular simulations guided by Raman spectroscopy. Phys. Chem. Chem. Phys.. 22:24014-24027.
.
2020. Scalable molecular dynamics on CPU and GPU architectures with NAMD. The Journal of Chemical Physics. 153
.
2018. A Streamlined, General Approach for Computing Ligand Binding Free Energies and Its Application to GPCR-Bound Cholesterol.. Journal of Chemical Theory and Computation. 14:6560–6573.
.
2017. A membrane-inserted structural model of the yeast mitofusin Fzo1. Sci Rep. 7(1):10217.
.
2017. New Coarse Variables for the Accurate Determination of Standard Binding Free Energies. J Chem Theory Comput. 13(11):5173-5178.
.
2017. Smoothed biasing forces yield unbiased free energies with the extended-system Adaptive Biasing Force method. J. Phys. Chem. B. 121(15):3676–3685.
.
2016. Evolution of Pentameric Ligand-Gated Ion Channels: Pro-Loop Receptors.. Plos One. 11:e0151934.
.
2015. The adaptive biasing force method: everything you always wanted to know but were afraid to ask.. J. Phys. Chem. B. 119:1129–51.
.
2015. Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory.. J. Membr. Biol.. 248
.
2015. Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains.. J. Phys. Chem. B. 119:8939–49.
.
2014. Allosteric regulation of pentameric ligand-gated ion channels: An emerging mechanistic perspective. Channels. 8:350–360.
.
2014. CHARMM36 united atom chain model for lipids and surfactants.. J. Phys. Chem. B. 118:547–556.
.
2014. Foundations of Biomolecular Simulations: A Critical Introduction to Homology Modeling, Molecular Dynamics Simulations, and Free Energy Calculations of Membrane Proteins. Membrane Proteins Production for Structural Analysis. :347–392.
.
2014. Lipid concentration and molar ratio boundaries for the use of isotropic bicelles.. Langmuir. 30:6162–6170.