An algorithm to enumerate all possible protein conformations verifying a set of distance constraints.

ABSTRACT:

Background

The determination of protein structures satisfying distance constraints is an important problem in structural biology. Whereas the most common method currently employed is simulated annealing, there have been other methods previously proposed in the literature. Most of them, however, are designed to find one solution only.

Results

In order to explore exhaustively the feasible conformational space, we propose here an interval Branch-and-Prune algorithm (iBP) to solve the Distance Geometry Problem (DGP) associated to protein structure determination. This algorithm is based on a discretization of the problem obtained by recursively constructing a search space having the structure of a tree, and by verifying whether the generated atomic positions are feasible or not b

SUBMITTER: Cassioli A 

PROVIDER: S-EPMC4384350 | biostudies-literature | 2015 Jan

REPOSITORIES: biostudies-literature