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Dataset for "Optimal Enhanced Sampling of Protein Conformational Changes by Extract Reaction Coordinates from Energy Relaxation"

dataset
posted on 2023-07-28, 15:47 authored by Kenneth TsuiKenneth Tsui, Ao MaAo Ma, Huiyu Li

This set of files contain the data generated in the paper titled: Optimal Enhanced Sampling of Protein Conformational Changes by Extract Reaction Coordinates from Energy Relaxation. The RC-uncovered trajectories along the leading SCs of HIV protease and PDZ2 domain are available here. Also listed are the natural trajectories for ligand dissociation in HIV protease and PDZ2 domain that correspond to supplementary videos S3, S4 and S5. In each case, .xtc files are trajectory files in GROMACS format, the .py file is the corresponding UCSF Chimera file and the .cxs file is the corresponding ChimeraX file. ChimeraX is the latest upgrade of Chimera. In each Chimera or ChimeraX file, the structure in white color is a equilibrated structure from MD simulation, which is used as reference for comparison.

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