The SBASE protein domain library, release 9.0: An online resource for protein domain identification

Abstract

SBASE (http://www.icgeb.trieste.it/sbase) is an online resource of protein domain sequences designed to facilitate detection of domain homologies based on a simple database search. The ninth release of the SBASE library of protein domain sequences contains 320 000 annotated structural, functional, ligand-binding and topogenic segments of proteins clustered into over 3481 domain groups and 483 protein families. Domain identification and functional prediction are based on a comparison of BLAST search outputs with a knowledge base of within-group ('self') and out-of-group ('non-self') similarities of the known domain groups. This is a memory-based approach wherein class-specific similarity functions are automatically learned from the database [Stanfill, C. and Waltz, D.