Structure prediction of loops with fixed and flexible stems.

ABSTRACT: The prediction of loop structures is considered one of the main challenges in the protein folding problem. Regardless of the dependence of the overall algorithm on the protein data bank, the flexibility of loop regions dictates the need for special attention to their structures. In this article, we present algorithms for loop structure prediction with fixed stem and flexible stem geometry. In the flexible stem geometry problem, only the secondary structure of three stem residues on either side of the loop is known. In the fixed stem geometry problem, the structure of the three stem residues on either side of the loop is also known. Initial loop structures are generated using a probability database for the flexible stem geometry problem, and using torsion angle dynamics for the fixed stem g

SUBMITTER: Subramani A 

PROVIDER: S-EPMC3376179 | biostudies-literature | 2012 Jun

REPOSITORIES: biostudies-literature