title: PIRSF: family classification system at the Protein Information Resource.
abstract: The Protein Information Resource (PIR) is an integrated public resource of protein informatics. To facilitate the sensible propagation and standardization of protein annotation and the systematic detection of annotation errors, PIR has extended its superfamily concept and developed the SuperFamily (PIRSF) classification system. Based on the evolutionary relationships of whole proteins, this classification system allows annotation of both specific biological and generic biochemical functions. The system adopts a network structure for protein classification from superfamily to subfamily levels. Protein family members are homologous (sharing common ancestry) and homeomorphic (sharing full-length sequence similarity with common domain architecture). The PIRSF database consists of two data sets, preliminary clusters and curated families. The curated families include family name, protein membership, parent-child relationship, domain architecture, and optional description and bibliography. PIRSF is accessible from the website at http://pir.georgetown.edu/pirsf/ for report retrieval and sequence classification. The report presents family annotation, membership statistics, cross-references to other databases, graphical display of domain architecture, and links to multiple sequence alignments and phylogenetic trees for curated families. PIRSF can be utilized to analyze phylogenetic profiles, to reveal functional convergence and divergence, and to identify interesting relationships between homeomorphic families, domains and structural classes.
authors.affiliation: Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Road, NW, Box 571414, Washington, DC 20057-1414, USA. pirmail@georgetown.edu
authors.forename: Cathy H
authors.initials: CH
authors.lastname: Wu
authors.forename: Anastasia
authors.initials: A
authors.lastname: Nikolskaya
authors.forename: Hongzhan
authors.initials: H
authors.lastname: Huang
authors.forename: Lai-Su L
authors.initials: LS
authors.lastname: Yeh
authors.forename: Darren A
authors.initials: DA
authors.lastname: Natale
authors.forename: C R
authors.initials: CR
authors.lastname: Vinayaka
authors.forename: Zhang-Zhi
authors.initials: ZZ
authors.lastname: Hu
authors.forename: Raja
authors.initials: R
authors.lastname: Mazumder
authors.forename: Sandeep
authors.initials: S
authors.lastname: Kumar
authors.forename: Panagiotis
authors.initials: P
authors.lastname: Kourtesis
authors.forename: Robert S
authors.initials: RS
authors.lastname: Ledley
authors.forename: Baris E
authors.initials: BE
authors.lastname: Suzek
authors.forename: Leslie
authors.initials: L
authors.lastname: Arminski
authors.forename: Yongxing
authors.initials: Y
authors.lastname: Chen
authors.forename: Jian
authors.initials: J
authors.lastname: Zhang
authors.forename: Jorge Louie
authors.initials: JL
authors.lastname: Cardenas
authors.forename: Sehee
authors.initials: S
authors.lastname: Chung
authors.forename: Jorge
authors.initials: J
authors.lastname: Castro-Alvear
authors.forename: Georgi
authors.initials: G
authors.lastname: Dinkov
authors.forename: Winona C
authors.initials: WC
authors.lastname: Barker
mesh_terms: D020816:Amino Acid Motifs; D000818:Animals; D019295:Computational Biology; D030562:Databases, Protein; D019143:Evolution, Molecular; D006801:Humans; D016247:Information Storage and Retrieval; D020407:Internet; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000145:classification*
chemical_list: D011506:Proteins