Prediction of Long Loops with Embedded Secondary Structure using the Protein Local Optimization Program.

ABSTRACT: Robust homology modeling to atomic-level accuracy requires in the general case successful prediction of protein loops containing small segments of secondary structure. Further, as loop prediction advances to success with larger loops, the exclusion of loops containing secondary structure becomes awkward. Here, we extend the applicability of the Protein Local Optimization Program (PLOP) to loops up to 17 residues in length that contain either helical or hairpin segments. In general, PLOP hierarchically samples conformational space and ranks candidate loops with a high-quality molecular mechanics force field. For loops identified to possess α-helical segments, we employ an alternative dihedral library composed of (ϕ,ψ) angles commonly found in helices. The alternative library is searc

SUBMITTER: Miller EB 

PROVIDER: S-EPMC3694628 | biostudies-literature | 2013 Mar

REPOSITORIES: biostudies-literature