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

Nucleic Acids Res. 2002 Jan 1;30(1):273-5. doi: 10.1093/nar/30.1.273.

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. (1986) COMMUN: ACM, 29, 1213-1228].

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Computer Graphics
  • Databases, Protein*
  • Information Storage and Retrieval
  • Internet
  • Ligands
  • Protein Structure, Tertiary*
  • Proteins / chemistry*
  • Proteins / physiology
  • Sequence Homology, Amino Acid
  • Structure-Activity Relationship

Substances

  • Ligands
  • Proteins