Memory kernel extraction and mean first-passage time for fast-folding proteins (Q - trajectories)

Fraction of native contacts reaction coordinate (Q) trajectories for the 8 proteins that appear in the Dalton et. al. PNAS 2023. For the original all-atom data from which the Q(t) were calculated, contact the group of David E. Shaw at Shaw Research (see the paper - K. Lindorff-Larsen, S. Piana, R. O. Dror, D. E. Shaw, How fast-folding proteins fold. Science 334, 517–520 (2011)) Data contains: - Q(t) trajectories for 8 proteins - Corresponding free energy profiles Example analysis codes (written in C++) are included for: - Free energy calculation - Mean first-passage times - Velocity-velocity correlation function and position-force correlation function calculations, needed for memory kernel extraction - Memory kernel extraction (see Ayaz et. al. PNAS 2021)

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Freie Universität Berlin
Germany

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