Abstract
BackgroundSmall 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.DescriptionThe 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.ConclusionMotivated 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.
Highlights
Small loop-shaped motifs are common constituents of the three-dimensional structure of proteins
BMC Bioinformatics 2009, 10:60 http://www.biomedcentral.com/1471-2105/10/60 right, as they can be defined in terms of their dihedral angles and hydrogen-bond, in the absence of any knowledge of the secondary structure
Full details of the database schema and tables are available as Additional files 2 and 3 – here we describe the construction pipeline for the key information in the database (Fig. 1): We have constructed a relational database of these motifs that can be interrogated using Structured Query Language (SQL)
Summary
Understanding of the diverse three-dimensional structures of proteins is aided by the recognition of their structural components. Construction of the Motivated Proteins web application We have used Java servlet technology to provide web access to the Protein Motif database, the servlet currently running in a Sun Java System Web Server (version 7.0) on the same machine as the Protein Motif database It generates the main XHTML query pages (level 1.0 Strict) with which the user interacts (Utility section). Included.) Alternatively, a keyword search can be performed to find proteins in the database answering a specific description (Fig. 2b–d) In both cases considered above it can happen that the user makes a query for a motif, only to find that there are no instances of that motif in the protein selected. If the focus is a particular motif, the user is able to employ the 'Specific Motifs' menu option
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