Estimation of protein folding probability from equilibrium simulations

Francesco Rao; Giovanni Settanni; Enrico Guarnera; Amedeo Caflisch

doi:10.1063/1.1893753

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Estimation of protein folding probability from equilibrium simulations

Francesco Rao·Giovanni Settanni·Enrico Guarnera·Amedeo Caflisch

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Abstract

The assumption that similar structures have similar folding probabilities ($p_{fold}$) leads naturally to a procedure to evaluate $p_{fold}$ for every snapshot saved along an equilibrium folding-unfolding trajectory of a structured peptide or protein. The procedure utilizes a structurally homogeneous clustering and does not require any additional simulation. It can be used to detect multiple folding pathways as shown for a three-stranded antiparallel $β$-sheet peptide investigated by implicit solvent molecular dynamics simulations.

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Francesco Rao, Giovanni Settanni, Enrico Guarnera, Amedeo Caflisch. 2005-03-10. Estimation of protein folding probability from equilibrium simulations. https://doi.org/10.1063/1.1893753

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