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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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Won, Sang Joon; Davda, Dahvid; Labby, Kristin J et al. (2016) Molecular Mechanism for Isoform-Selective Inhibition of Acyl Protein Thioesterases 1 and 2 (APT1 and APT2). ACS Chem Biol 11:3374-3382
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Mustoe, Anthony M; Al-Hashimi, Hashim M; Brooks 3rd, Charles L (2016) Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme. Nucleic Acids Res 44:402-12
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Lee, Jumin; Cheng, Xi; Swails, Jason M et al. (2016) CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. J Chem Theory Comput 12:405-13
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