Estimation of protein folding probability from equilibrium simulations.
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.
Rao
Francesco
F
Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
Settanni
Giovanni
G
Guarnera
Enrico
E
Caflisch
Amedeo
A
D001703:Biophysics / Q000379:methods*; D002627:Chemistry, Physical / Q000379:methods*; D016000:Cluster Analysis; D008958:Models, Molecular; D015233:Models, Statistical; D008962:Models, Theoretical; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry; D011336:Probability; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013997:Time Factors
D010455:Peptides; D011506:Proteins