PDZBase: a protein–protein interaction database for PDZ-domains

• Published in: Bioinformatics Vol. 21; no. 6; pp. 827 - 828
• Main Authors: Beuming, Thijs, Skrabanek, Lucy, Niv, Masha Y., Mukherjee, Piali, Weinstein, Harel
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 15.03.2005; Oxford Publishing Limited (England)
• Subjects: Biological and medical sciences; Database Management Systems; Databases, Protein; Fundamental and applied biological sciences. Psychology; General aspects; Information Storage and Retrieval - methods; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Membrane Proteins - chemistry; Membrane Proteins - metabolism; Natural Language Processing; Periodicals as Topic; Protein Interaction Mapping - methods; Protein Structure, Tertiary; User-Computer Interface; Vocabulary, Controlled; Database; Molecular interaction; Keyword; Secondary structure; Bioinformatics; Aminoacid sequence
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/bti098

PDZBase is a database that aims to contain all known PDZ-domain-mediated protein–protein interactions. Currently, PDZBase contains approximately 300 such interactions, which have been manually extracted from >200 articles. The database can be queried through both sequence motif and keyword-based searches, and the sequences of interacting proteins can be visually inspected through alignments (for the comparison of several interactions), or as residue-based diagrams including schematic secondary structure information (for individual complexes). Availability: http://icb.med.cornell.edu/services/pdz/start. Contact: pdzbase@med.cornell.edu.