Estimation of protein folding probability from equilibrium simulations

Details Estimation of protein folding probability from equilibrium simulations Estimation of protein folding probability from equilibrium simulations

2005-03-10

arxiv.org/abs/q-bio/0503014v1

Biology

Quantitative Biology

Biomolecules

7 pages, 4 figures, supplemetary materials

Scientific paper

10.1063/1.1893753

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 $\beta$-sheet peptide investigated by implicit solvent molecular dynamics simulations.

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