KNOTTIN: the database of inhibitor cystine knot scaffold after 10 years, toward a systematic structure modeling

• Published in: Nucleic acids research Vol. 46; no. D1; pp. D454 - D458
• Main Authors: Postic, Guillaume, Gracy, Jérôme, Périn, Charlotte, Chiche, Laurent, Gelly, Jean-Christophe
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 04.01.2018
• Subjects: Amino Acid Sequence; Computer Graphics; Cystine-Knot Miniproteins - chemistry; Cystine-Knot Miniproteins - classification; Cystine-Knot Miniproteins - genetics; Cystine-Knot Miniproteins - metabolism; Database Issue; Databases, Protein - history; Disulfides; Gene Expression; History, 21st Century; Humans; Internet; Ligands; Models, Molecular; Protein Conformation, alpha-Helical; Protein Conformation, beta-Strand; Sequence Alignment; Sequence Analysis, Protein; User-Computer Interface
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkx1084

Abstract Knottins, or inhibitor cystine knots (ICKs), are ultra-stable miniproteins with multiple applications in drug design and medical imaging. These widespread and functionally diverse proteins are characterized by the presence of three interwoven disulfide bridges in their structure, which form a unique pseudoknot. Since 2004, the KNOTTIN database (www.dsimb.inserm.fr/KNOTTIN/) has been gathering standardized information about knottin sequences, structures, functions and evolution. The website also provides access to bibliographic data and to computational tools that have been specifically developed for ICKs. Here, we present a major upgrade of our database, both in terms of data content and user interface. In addition to the new features, this article describes how KNOTTIN has seen its size multiplied over the past ten years (since its last publication), notably with the recent inclusion of predicted ICKs structures. Finally, we report how our web resource has proved usefulness for the researchers working on ICKs, and how the new version of the KNOTTIN website will continue to serve this active community.