Estimation of protein folding probability from equilibrium simulations
| Title | Estimation of protein folding probability from equilibrium simulations |
| Publication Type | Journal Article |
| Year of Publication | 2005 |
| Authors | Rao F., Settanni G., Guarnera E., Caflisch A. |
| Journal | Journal of Chemical Physics |
| Volume | 122 |
| Issue | 18 |
| Pagination | 184901 |
| Date Published | 2005 May 8 |
| Type of Article | Research Article |
| Keywords | Biophysics, Chemistry, Physical, Cluster Analysis, Models, Molecular, Models, Statistical, Models, Theoretical, Monte Carlo Method, Peptides, Probability, Protein Folding, Protein Structure, Secondary, Proteins, Time Factors |
| Abstract | The assumption that similar structures have similar folding probabilities (pfold) leads naturally to a procedure to evaluate pfold 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. |
| DOI | 10.1063/1.1893753 |
| pubindex | 0066 |
| Alternate Journal | J Chem Phys |
| PubMed ID | 15918759 |
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