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Resource:CAPS Database

Name: Resource:CAPS Database
Description: CAPS - Database (CAPS-DB) is a structural classification of helix-cappings or caps compiled from protein structures. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps. CASP-DB is fully browsable and searchable and is regularly updated.


The regions of the polypeptide chain immediately preceding or following an α-helix are known as Nt- and Ct cappings, respectively. Cappings play a central role stabilizing α-helices due to lack of intrahelical hydrogen bonds in the first and last turn. Sequence patterns of amino acid type preferences have been derived for cappings but the structural motifs associated to them are still unclassified. CAPS-DB is a database of clusters of structural patterns of different capping types. The clustering algorithm is based in the geometry and the (Φ-ψ)-space conformation of these regions. CAPS-DB is a relational database that allows the user to search, browse, inspect and retrieve structural data associated to cappings. The contents of CAPS-DB might be of interest to a wide range of scientist covering different areas such as protein design and engineering, structural biology and bioinformatics.

CapsDB v4.0

  • PDB structures: 4591
  • Number of clusters: 859
  • Number of caps: 31452[1]
Other Name(s): CAPS - Database
Abbreviation: CAPS-DB
Parent Organization: Aberystwyth University; Wales; United Kingdom
Supporting Agency: Research Councils United Kingdom, Leeds Institute of Molecular Medicine, MICINN, FEDER
Grant: BIO2011-22568
Resource Type(s): Database
Resource: Resource
URL: http://www.bioinsilico.org/CAPSDB
*Id: nlx_149414
PMID: PMID 22021380
Related to: Resource:PDB
Address: Institute of Biological, Environmental and Rural Science, Aberystwyth University, Goggerddan Campus, Aberystwyth SY23 3EB, United Kingdom
Keywords: structural classification, helix-capping, protein engineering, clustering
Link to OWL / RDF: Download this content as OWL/RDF

Curation status: Uncurated

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References

  1. Segura J et al. (2012) CAPS-DB: a structural classification of helix-capping motifs. Nucleic Acids Res 40: D479-85 PubMed

Notes

This page uses this default form:Resource

Alt. URL: http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home

Contributors

Aarnaud, Akash, Zaidaziz



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Facts about Resource:CAPS DatabaseRDF feed
AbbrevCAPS-DB  +
AddressInstitute of Biological  +, Environmental and Rural Science  +, Aberystwyth University  +, Goggerddan Campus  +, Aberystwyth SY23 3EB  +, and United Kingdom  +
AuthorsSegura J  +, Oliva B  +, and Fernandez-Fuentes N.  +
CurationStatuscurated  +
DefiningCitationhttp://www.bioinsilico.org/CAPSDB  +
DefinitionCAPS - Database (CAPS-DB) is a structural CAPS - Database (CAPS-DB) is a structural classification of helix-cappings or caps compiled from protein structures. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps. CASP-DB is fully browsable and searchable and is regularly updated.


The regions of the polypeptide chain immediately preceding or following an α-helix are known as Nt- and Ct cappings, respectively. Cappings play a central role stabilizing α-helices due to lack of intrahelical hydrogen bonds in the first and last turn. Sequence patterns of amino acid type preferences have been derived for cappings but the structural motifs associated to them are still unclassified. CAPS-DB is a database of clusters of structural patterns of different capping types. The clustering algorithm is based in the geometry and the (Φ-ψ)-space conformation of these regions. CAPS-DB is a relational database that allows the user to search, browse, inspect and retrieve structural data associated to cappings. The contents of CAPS-DB might be of interest to a wide range of scientist covering different areas such as protein design and engineering, structural biology and bioinformatics.

CapsDB v4.0

  • PDB structures: 4591
  • Number of clusters: 859
  • Number of caps: 31452 r of clusters: 859
  • Number of caps: 31452
ExampleImageCAPS Database.PNG  +
Figure4  +
GrantCategory:BIO2011-22568   +
Has default formThis property is a special property in this wiki.Resource  +
Has roleDatabase  +
Idnlx_149414  +
Is part ofAberystwyth University; Wales; United Kingdom  +
JournalVolume40  +
KeywordsStructural classification  +, Helix-capping  +, Protein engineering  +, and Clustering  +
LabelResource:CAPS Database  +
ModifiedDate5 September 2012  +
PMID22021380  +
Page has default formThis property is a special property in this wiki.Resource  +
Pages479-85
PublicationDate2011 Oct 22.  +
PublicationNameNucleic Acid Research  +
RelatedToResource:PDB  +
SuperCategoryResource  +
Supporting AgencyResearch Councils United Kingdom  +, Leeds Institute of Molecular Medicine  +, MICINN  +, and FEDER  +
SynonymCAPS - Database  +
TitleCAPS-DB: a structural classification of helix-capping motifs.  +