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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

Sequence logo (25) for the alignment of all standardized sequences in the KNOTTIN database. The alignment is truncated between the first and the last cysteine of the knot (standard positions 20 and 100, respectively).
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Figure 1: Sequence logo (25) for the alignment of all standardized sequences in the KNOTTIN database. The alignment is truncated between the first and the last cysteine of the knot (standard positions 20 and 100, respectively).

Mentions: Other improvements of the KNOTTIN website are, e.g. the availability of alignments in various text formats for downloads and of sequence logos (25). The logo for the entire database content is shown in Figure 1 and the percent of identity between knottins in Figure 2.Figure 1.


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)

Sequence logo (25) for the alignment of all standardized sequences in the KNOTTIN database. The alignment is truncated between the first and the last cysteine of the knot (standard positions 20 and 100, respectively).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 1: Sequence logo (25) for the alignment of all standardized sequences in the KNOTTIN database. The alignment is truncated between the first and the last cysteine of the knot (standard positions 20 and 100, respectively).
Mentions: Other improvements of the KNOTTIN website are, e.g. the availability of alignments in various text formats for downloads and of sequence logos (25). The logo for the entire database content is shown in Figure 1 and the percent of identity between knottins in Figure 2.Figure 1.

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