MALISAM: a database of structurally analogous motifs in proteins.

ABSTRACT: MALISAM (manual alignments for structurally analogous motifs) represents the first database containing pairs of structural analogs and their alignments. To find reliable analogs, we developed an approach based on three ideas. First, an insertion together with a part of the evolutionary core of one domain family (a hybrid motif) is analogous to a similar motif contained within the core of another domain family. Second, a motif at an interface, formed by secondary structural elements (SSEs) contributed by two or more domains or subunits contacting along that interface, is analogous to a similar motif present in the core of a single domain. Third, an artificial protein obtained through selection from random peptides or in sequence design experiments not biased by sequences of a particular hom

SUBMITTER: Cheng H 

PROVIDER: S-EPMC2238938 | biostudies-literature | 2008 Jan

REPOSITORIES: biostudies-literature