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Vilseck, Jonah Z; Armacost, Kira A; Hayes, Ryan L et al. (2018) Predicting Binding Free Energies in a Large Combinatorial Chemical Space Using Multisite ? Dynamics. J Phys Chem Lett 9:3328-3332
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Hayes, Ryan L; Vilseck, Jonah Z; Brooks 3rd, Charles L (2018) Approaching protein design with multisite ? dynamics: Accurate and scalable mutational folding free energies in T4 lysozyme. Protein Sci 27:1910-1922
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Ding, Xinqiang; Hayes, Ryan L; Vilseck, Jonah Z et al. (2018) CDOCKER and ?-dynamics for prospective prediction in D?R Grand Challenge 2. J Comput Aided Mol Des 32:89-102
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Ding, Xinqiang; Vilseck, Jonah Z; Hayes, Ryan L et al. (2017) Gibbs Sampler-Based ?-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation. J Chem Theory Comput 13:2501-2510
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Su, Min; Guo, Emily Z; Ding, Xinqiang et al. (2017) Mechanism of Vps4 hexamer function revealed by cryo-EM. Sci Adv 3:e1700325
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Hayes, Ryan L; Armacost, Kira A; Vilseck, Jonah Z et al. (2017) Adaptive Landscape Flattening Accelerates Sampling of Alchemical Space in Multisite ? Dynamics. J Phys Chem B 121:3626-3635
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Kim, Seonghoon; Lee, Jumin; Jo, Sunhwan et al. (2017) CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules. J Comput Chem 38:1879-1886
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Bruno, Paul A; Morriss-Andrews, Alex; Henderson, Andrew R et al. (2016) A Synthetic Loop Replacement Peptide That Blocks Canonical NF-?B Signaling. Angew Chem Int Ed Engl 55:14997-15001
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Soteras Gutiérrez, Ignacio; Lin, Fang-Yu; Vanommeslaeghe, Kenno et al. (2016) Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand-protein interactions. Bioorg Med Chem 24:4812-4825
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Gagnon, Jessica K; Law, Sean M; Brooks 3rd, Charles L (2016) Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM. J Comput Chem 37:753-62
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Showing the most recent 10 out of 93 publications
