The Protein Information Resource

Abstract

The Protein Information Resource (PIR) is an integrated public resource of protein informatics that supports genomic and proteomic research and scientific discovery. PIR maintains the Protein Sequence Database (PSD), an annotated protein database containing over 283 000 sequences covering the entire taxonomic range. Family classification is used for sensitive identification, consistent annotation, and detection of annotation errors. The superfamily curation defines signature domain architecture and categorizes memberships to improve automated classification. To increase the amount of experimental annotation, the PIR has developed a bibliography system for literature searching, mapping, and user submission, and has conducted retrospective attribution of citations for experimental features. PIR also maintains NREF, a non-redundant reference database, and iProClass, an integrated database of protein family, function, and structure information. PIR-NREF provides a timely and comprehensive collection of protein sequences, currently consisting of more than 1 000 000 entries from PIR-PSD, SWISS-PROT, TrEMBL, RefSeq, GenPept, and PDB. The PIR web site (http://pir.georgetown.edu) connects data analysis tools to underlying databases for information retrieval and knowledge discovery, with functionalities for interactive queries, combinations of sequence and text searches, and sorting and visual exploration of search results. The FTP site provides free download for PSD and NREF biweekly releases and auxiliary databases and files.

Systematic identification of cancer-specific MHC-binding peptides with RAVEN

“…35 RAVEN automatically crosschecked these peptides by a text search algorithm with ApacheLucene 36,37 against the human reference-proteome (UniProt release 2015_06) to exclude sequence identity with non-specifically expressed proteins. In total, RAVEN predicted 7247 9-mer peptides with high MHC-I-affinity (defined as a dissociation constant K d ≤ 150 nM) of which 6589 had no sequence identity with any other protein (Supplementary Table 6).…”

“…30,31 The peptide search service 36 of UniProt is queried via a RESTful web service which API is provided and integrated by Protein Information Resource (PIR) using ApacheLucene for peptide text searches. 36,37 In RAVEN, this approach is available for the most common alleles in human and mouse. In contrast to other methods provided by RAVEN, this pipeline is independent from the analyzed gene expression dataset but requires an internet connection.…”

NMR structure of protein yqbG from Bacillus subtilis reveals a novel α‐helical protein fold

“…All three proteins belong to PIRSF family SF007500. 3 So far, no functional annotations are available. Here we report the high-quality NMR solution structure of protein yqbG,, which exhibits a novel ␣-helical fold.…”

“…Spectra were processed and analyzed with the programs PROSA 8 and XEASY 9 , respectively. Sequence specific backbone (H N , H ␣ , N, C ␣ ) and H ␤ /C ␤ resonance assignments were obtained by using (4,3)…”

“…7 Assignments were obtained for 100% of the assignable backbone (excluding the N-terminal NH 3 ϩ , the Pro 15 N and the 13 CЈ shifts) and 13 Table I). Stereospecific assignments were obtained for 55% of the ␤-methylene groups exhibiting nondegenerated proton chemical shifts and for 80% of the Val and Leu isopropyl moieties (Table I).…”