Connectivity independent protein-structure alignment: a hierarchical approach.

ABSTRACT:

Background

Protein-structure alignment is a fundamental tool to study protein function, evolution and model building. In the last decade several methods for structure alignment were introduced, but most of them ignore that structurally similar proteins can share the same spatial arrangement of secondary structure elements (SSE) but differ in the underlying polypeptide chain connectivity (non-sequential SSE connectivity).

Results

We perform protein-structure alignment using a two-level hierarchical approach implemented in the program GANGSTA. On the first level, pair contacts and relative orientations between SSEs (i.e. alpha-helices and beta-strands) are maximized with a genetic algorithm (GA). On the second level residue pair contacts from the best SSE alignments are optimi

SUBMITTER: Kolbeck B 

PROVIDER: S-EPMC1683948 | biostudies-literature | 2006 Nov

REPOSITORIES: biostudies-literature