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PMID: 14681383 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

The KNOTTIN website and database: a new information system dedicated to the knottin scaffold.

Nucleic acids research ·Vol. 32 ·No. Database issue ·2004-01-01 ·Pages D156-9

Gelly JC, Gracy J, Kaas Q, Le-Nguyen D, Heitz A, Chiche L

Abstract

The KNOTTIN website and database organize information about knottins or inhibitor cystine knots, small disulfide-rich proteins with a knotted topology. Thanks to their small size and high stability, knottins provide appealing scaffolds for protein engineering and drug design. Static pages present the main historical and recent results about knottin discoveries, sequences, structures, folding, functions, applications and bibliography. Database searches provide dynamically generated tabular reports or sequence alignments for knottin three-dimensional structures or sequences. BLAST/HMM searches are also available. A simple nomenclature, based on loop lengths between cysteines, is proposed and is complemented by a uniform numbering scheme. This standardization is applied to all knottin structures in the database, facilitating comparisons. Renumbered and structurally fitted knottin PDB files are available for download. The standardized numbering is used for automatic drawing of two-dimensional Colliers de Perles. The KNOTTIN website and database are available at http://knottin.cbs.cnrs.fr and http://knottin.com.

MeSH Terms

Amino Acid Motifs Amino Acid Sequence Animals Computational Biology Cystine/chemistry Databases, Protein Disulfides/chemistry Humans Information Storage and Retrieval Internet Molecular Sequence Data Protein Structure, Tertiary Proteins/chemistry,metabolism Structure-Activity Relationship Terminology as Topic

Chemicals

Disulfides Proteins Cystine

Authors & Affiliations

6 authors, click to expand affiliations / ORCID

Gelly Jean-Christophe

Centre de Biochimie Structurale, UMR 5048 CNRS INSERM Université Montpellier I, Faculté de Pharmacie, 15 avenue Charles Flahault, F-34093 Montpellier, France.

Gracy Jérôme

Kaas Quentin

Le-Nguyen Dung

Heitz Annie

Chiche Laurent

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20 references, click to expand

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Article Info

Journal

Nucleic acids research

Abbr.

Nucleic Acids Res

ISSN

1362-4962

DOI

10.1093/nar/gkh015

Published

2004-01-01

Pages

D156-9

Language

English

Region

England

NLM ID

0411011

PMCID

PMC308750

Subset

Databases

PDB

2BTC

External Links

PubMed source DOI: 10.1093/nar/gkh015 PMC Full Text View journal details

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