title: PEP: Predictions for Entire Proteomes.
abstract: PEP is a database of Predictions for Entire Proteomes. The database contains summaries of analyses of protein sequences from a range of organisms representing all three major kingdoms of life: eukaryotes, prokaryotes and archaea. All proteins publicly available for organisms were aligned against SWISS-PROT, TrEMBL and PDB. Additionally, the following annotations are provided: secondary structure, transmembrane helices, coiled coils, regions of low complexity, signal peptides, PROSITE motifs, nuclear localization signals and classes of cellular function. Proteins that contain long regions without regular secondary structure are also identified. We have produced a related database of structural domain-like fragments derived from PEP and clusters based on homology between all fragments. The PEP database, fragments and clusters are distributed freely as a set of flat files and have been integrated into SRS. The PEP group of databases can be accessed from: http://cubic.bioc.columbia.edu/pep.
authors.affiliation: CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA. carter@cubic.bioc.columbia.edu
authors.forename: Phil
authors.initials: P
authors.lastname: Carter
authors.forename: Jinfeng
authors.initials: J
authors.lastname: Liu
authors.forename: Burkhard
authors.initials: B
authors.lastname: Rost
mesh_terms: D000818:Animals; D019843:Archaeal Proteins / Q000737:chemistry; D016000:Cluster Analysis; D030562:Databases, Protein; D005057:Eukaryotic Cells; D006801:Humans; D011387:Prokaryotic Cells; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry; D020543:Proteome / Q000737:chemistry* / Q000502:physiology; D017386:Sequence Homology, Amino Acid; D014584:User-Computer Interface
chemical_list: D019843:Archaeal Proteins; D011506:Proteins; D020543:Proteome