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KNOTTIN: the knottin or inhibitor cystine knot scaffold in 2007.

Gracy J, Le-Nguyen D, Gelly JC, Kaas Q, Heitz A, Chiche L - Nucleic Acids Res. (2007)

Bottom Line: Therefore, the whole KNOTTIN database (sequences and structures) can now be searched using loop lengths, in addition to keyword and sequence (BLAST, HMMER) searches.Renumbered and structurally fitted knottin PDB files are available for download as well as renumbered sequences, sequence alignments and logos.The knottin numbering scheme is used for automatic drawing of standardized two-dimensional Colliers de Perles of any knottin structure or sequence in the database or provided by the user.

View Article: PubMed Central - PubMed

Affiliation: Université de Montpellier, CNRS, UMR5048, Centre de Biochimie Structurale, 34090 Montpellier, INSERM, U554, Montpellier, France.

ABSTRACT
The KNOTTIN database provides standardized information on the small disulfide-rich proteins with a knotted topology called knottins or inhibitor cystine knots. Static pages present the essential historical or recent results about knottin discoveries, sequences, structures, syntheses, folding, functions, applications and bibliography. New tools, KNOTER3D and KNOTER1D, are provided to determine or predict if a user query (3D structure or sequence) is a knottin. These tools are now used to automate the database update. All knottin structures and sequences in the database are now standardized according to the knottin nomenclature based on loop lengths between knotted cysteines, and to the knottin numbering scheme. Therefore, the whole KNOTTIN database (sequences and structures) can now be searched using loop lengths, in addition to keyword and sequence (BLAST, HMMER) searches. Renumbered and structurally fitted knottin PDB files are available for download as well as renumbered sequences, sequence alignments and logos. The knottin numbering scheme is used for automatic drawing of standardized two-dimensional Colliers de Perles of any knottin structure or sequence in the database or provided by the user. The KNOTTIN database is available at http://knottin.cbs.cnrs.fr.

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Related in: MedlinePlus

Statistics on loop lengths in the KNOTTIN database. Loop labels follow the knottin nomenclature (3).
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Related In: Results  -  Collection

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Figure 3: Statistics on loop lengths in the KNOTTIN database. Loop labels follow the knottin nomenclature (3).

Mentions: The sequence database can now be searched or sorted using criteria based on loop lengths. This allows, e.g. to easily establish exhaustive statistics on loop lengths including different unrelated families. Such statistics are displayed in Figure 3 and now appear on the database homepage. In previous releases, only the 3D structures were standardized.


KNOTTIN: the knottin or inhibitor cystine knot scaffold in 2007.

Gracy J, Le-Nguyen D, Gelly JC, Kaas Q, Heitz A, Chiche L - Nucleic Acids Res. (2007)

Statistics on loop lengths in the KNOTTIN database. Loop labels follow the knottin nomenclature (3).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238874&req=5

Figure 3: Statistics on loop lengths in the KNOTTIN database. Loop labels follow the knottin nomenclature (3).
Mentions: The sequence database can now be searched or sorted using criteria based on loop lengths. This allows, e.g. to easily establish exhaustive statistics on loop lengths including different unrelated families. Such statistics are displayed in Figure 3 and now appear on the database homepage. In previous releases, only the 3D structures were standardized.

Bottom Line: Therefore, the whole KNOTTIN database (sequences and structures) can now be searched using loop lengths, in addition to keyword and sequence (BLAST, HMMER) searches.Renumbered and structurally fitted knottin PDB files are available for download as well as renumbered sequences, sequence alignments and logos.The knottin numbering scheme is used for automatic drawing of standardized two-dimensional Colliers de Perles of any knottin structure or sequence in the database or provided by the user.

View Article: PubMed Central - PubMed

Affiliation: Université de Montpellier, CNRS, UMR5048, Centre de Biochimie Structurale, 34090 Montpellier, INSERM, U554, Montpellier, France.

ABSTRACT
The KNOTTIN database provides standardized information on the small disulfide-rich proteins with a knotted topology called knottins or inhibitor cystine knots. Static pages present the essential historical or recent results about knottin discoveries, sequences, structures, syntheses, folding, functions, applications and bibliography. New tools, KNOTER3D and KNOTER1D, are provided to determine or predict if a user query (3D structure or sequence) is a knottin. These tools are now used to automate the database update. All knottin structures and sequences in the database are now standardized according to the knottin nomenclature based on loop lengths between knotted cysteines, and to the knottin numbering scheme. Therefore, the whole KNOTTIN database (sequences and structures) can now be searched using loop lengths, in addition to keyword and sequence (BLAST, HMMER) searches. Renumbered and structurally fitted knottin PDB files are available for download as well as renumbered sequences, sequence alignments and logos. The knottin numbering scheme is used for automatic drawing of standardized two-dimensional Colliers de Perles of any knottin structure or sequence in the database or provided by the user. The KNOTTIN database is available at http://knottin.cbs.cnrs.fr.

Show MeSH
Related in: MedlinePlus