Abstract
Interaction forces among residue pairs are determined from optimum folding pathways along which a protein represented as a coarse-grained chain of α-carbons goes from different initial configurations to a known native state. A dynamic optimization approach is employed that uses the coarse-grained model to compute the optimal folding pathways. The pair-wise interaction forces obtained in this manner are incorporated into the coarse-grained model which is then simulated to fold the protein from a new set of initial configurations in a predictive way. We show that the folding pathways predicted in this manner are near-optimal. We applied the technique to the secondary structures: helix and β-sheet.
Original language | English |
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Pages (from-to) | 1949-1961 |
Number of pages | 13 |
Journal | Physical Chemistry Chemical Physics |
Volume | 11 |
Issue number | 12 |
DOIs | |
Publication status | Published - 2009 |
Externally published | Yes |