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Motivated Proteins: A web application for studying small three-dimensional protein motifs

BACKGROUND: Small loop-shaped motifs are common constituents of the three-dimensional structure of proteins. Typically they comprise between three and seven amino acid residues, and are defined by a combination of dihedral angles and hydrogen bonding partners. The most abundant of these are αβ-motif...

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Detalles Bibliográficos
Autores principales: Leader, David P, Milner-White, E James
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651126/
https://www.ncbi.nlm.nih.gov/pubmed/19210785
http://dx.doi.org/10.1186/1471-2105-10-60
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author Leader, David P
Milner-White, E James
author_facet Leader, David P
Milner-White, E James
author_sort Leader, David P
collection PubMed
description BACKGROUND: Small loop-shaped motifs are common constituents of the three-dimensional structure of proteins. Typically they comprise between three and seven amino acid residues, and are defined by a combination of dihedral angles and hydrogen bonding partners. The most abundant of these are αβ-motifs, asx-motifs, asx-turns, β-bulges, β-bulge loops, β-turns, nests, niches, Schellmann loops, ST-motifs, ST-staples and ST-turns. We have constructed a database of such motifs from a range of high-quality protein structures and built a web application as a visual interface to this. DESCRIPTION: The web application, Motivated Proteins, provides access to these 12 motifs (with 48 sub-categories) in a database of over 400 representative proteins. Queries can be made for specific categories or sub-categories of motif, motifs in the vicinity of ligands, motifs which include part of an enzyme active site, overlapping motifs, or motifs which include a particular amino acid sequence. Individual proteins can be specified, or, where appropriate, motifs for all proteins listed. The results of queries are presented in textual form as an (X)HTML table, and may be saved as parsable plain text or XML. Motifs can be viewed and manipulated either individually or in the context of the protein in the Jmol applet structural viewer. Cartoons of the motifs imposed on a linear representation of protein secondary structure are also provided. Summary information for the motifs is available, as are histograms of amino acid distribution, and graphs of dihedral angles at individual positions in the motifs. CONCLUSION: Motivated Proteins is a publicly and freely accessible web application that enables protein scientists to study small three-dimensional motifs without requiring knowledge of either Structured Query Language or the underlying database schema.
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spelling pubmed-26511262009-03-05 Motivated Proteins: A web application for studying small three-dimensional protein motifs Leader, David P Milner-White, E James BMC Bioinformatics Database BACKGROUND: Small loop-shaped motifs are common constituents of the three-dimensional structure of proteins. Typically they comprise between three and seven amino acid residues, and are defined by a combination of dihedral angles and hydrogen bonding partners. The most abundant of these are αβ-motifs, asx-motifs, asx-turns, β-bulges, β-bulge loops, β-turns, nests, niches, Schellmann loops, ST-motifs, ST-staples and ST-turns. We have constructed a database of such motifs from a range of high-quality protein structures and built a web application as a visual interface to this. DESCRIPTION: The web application, Motivated Proteins, provides access to these 12 motifs (with 48 sub-categories) in a database of over 400 representative proteins. Queries can be made for specific categories or sub-categories of motif, motifs in the vicinity of ligands, motifs which include part of an enzyme active site, overlapping motifs, or motifs which include a particular amino acid sequence. Individual proteins can be specified, or, where appropriate, motifs for all proteins listed. The results of queries are presented in textual form as an (X)HTML table, and may be saved as parsable plain text or XML. Motifs can be viewed and manipulated either individually or in the context of the protein in the Jmol applet structural viewer. Cartoons of the motifs imposed on a linear representation of protein secondary structure are also provided. Summary information for the motifs is available, as are histograms of amino acid distribution, and graphs of dihedral angles at individual positions in the motifs. CONCLUSION: Motivated Proteins is a publicly and freely accessible web application that enables protein scientists to study small three-dimensional motifs without requiring knowledge of either Structured Query Language or the underlying database schema. BioMed Central 2009-02-11 /pmc/articles/PMC2651126/ /pubmed/19210785 http://dx.doi.org/10.1186/1471-2105-10-60 Text en Copyright © 2009 Leader and Milner-White; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database
Leader, David P
Milner-White, E James
Motivated Proteins: A web application for studying small three-dimensional protein motifs
title Motivated Proteins: A web application for studying small three-dimensional protein motifs
title_full Motivated Proteins: A web application for studying small three-dimensional protein motifs
title_fullStr Motivated Proteins: A web application for studying small three-dimensional protein motifs
title_full_unstemmed Motivated Proteins: A web application for studying small three-dimensional protein motifs
title_short Motivated Proteins: A web application for studying small three-dimensional protein motifs
title_sort motivated proteins: a web application for studying small three-dimensional protein motifs
topic Database
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651126/
https://www.ncbi.nlm.nih.gov/pubmed/19210785
http://dx.doi.org/10.1186/1471-2105-10-60
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