Estimation of protein folding probability from equilibrium simulations |
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Authors: | Rao Francesco Settanni Giovanni Guarnera Enrico Caflisch Amedeo |
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Institution: | Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland. |
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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 beta-sheet peptide investigated by implicit solvent molecular dynamics simulations. |
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