CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures.

ABSTRACT: We present CATHEDRAL, an iterative protocol for determining the location of previously observed protein folds in novel multidomain protein structures. CATHEDRAL builds on the features of a fast secondary-structure-based method (using graph theory) to locate known folds within a multidomain context and a residue-based, double-dynamic programming algorithm, which is used to align members of the target fold groups against the query protein structure to identify the closest relative and assign domain boundaries. To increase the fidelity of the assignments, a support vector machine is used to provide an optimal scoring scheme. Once a domain is verified, it is excised, and the search protocol is repeated in an iterative fashion until all recognisable domains have been identified. We have perform

SUBMITTER: Redfern OC 

PROVIDER: S-EPMC2098860 | biostudies-literature | 2007 Nov

REPOSITORIES: biostudies-literature