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Motivated proteins: a web application for studying small three-dimensional protein motifs.

Leader DP, Milner-White EJ - BMC Bioinformatics (2009)

Bottom Line: The results of queries are presented in textual form as an (X)HTML table, and may be saved as parsable plain text or XML.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK. d.leader@bio.gla.ac.uk

ABSTRACT

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 alphabeta-motifs, asx-motifs, asx-turns, beta-bulges, beta-bulge loops, beta-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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Schematic diagram of pipeline for constructing the database. The order of operations is indicated numerically. Database tables are shown with coloured backgrounds: primary entities (those with attributes derived directly by processing information in PDB files) are in claret (darker), entities derived by querying the primary entities and their relationships are in blue-green (brighter). Intermediate text files are not generally shown, nor is the manual addition of active site data to the residue entity, or the pruning of some of the type-1 β-turns described in the text.
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Figure 1: Schematic diagram of pipeline for constructing the database. The order of operations is indicated numerically. Database tables are shown with coloured backgrounds: primary entities (those with attributes derived directly by processing information in PDB files) are in claret (darker), entities derived by querying the primary entities and their relationships are in blue-green (brighter). Intermediate text files are not generally shown, nor is the manual addition of active site data to the residue entity, or the pruning of some of the type-1 β-turns described in the text.

Mentions: Because of the disparate size of motifs and the diversity of their defining features, we have adopted a database schema in which these features are not incorporated into a motif entity itself. Rather, they are embodied in the relationship of such a motif entity to an amino acid residue entity, and in the relationship of this residue entity to entities representing the atoms and hydrogen bonds of a protein. Thus, the database is fundamentally one that models the protein – the motifs are derived from this 'core database' by SQL queries, and then added to it. 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):


Motivated proteins: a web application for studying small three-dimensional protein motifs.

Leader DP, Milner-White EJ - BMC Bioinformatics (2009)

Schematic diagram of pipeline for constructing the database. The order of operations is indicated numerically. Database tables are shown with coloured backgrounds: primary entities (those with attributes derived directly by processing information in PDB files) are in claret (darker), entities derived by querying the primary entities and their relationships are in blue-green (brighter). Intermediate text files are not generally shown, nor is the manual addition of active site data to the residue entity, or the pruning of some of the type-1 β-turns described in the text.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651126&req=5

Figure 1: Schematic diagram of pipeline for constructing the database. The order of operations is indicated numerically. Database tables are shown with coloured backgrounds: primary entities (those with attributes derived directly by processing information in PDB files) are in claret (darker), entities derived by querying the primary entities and their relationships are in blue-green (brighter). Intermediate text files are not generally shown, nor is the manual addition of active site data to the residue entity, or the pruning of some of the type-1 β-turns described in the text.
Mentions: Because of the disparate size of motifs and the diversity of their defining features, we have adopted a database schema in which these features are not incorporated into a motif entity itself. Rather, they are embodied in the relationship of such a motif entity to an amino acid residue entity, and in the relationship of this residue entity to entities representing the atoms and hydrogen bonds of a protein. Thus, the database is fundamentally one that models the protein – the motifs are derived from this 'core database' by SQL queries, and then added to it. 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):

Bottom Line: The results of queries are presented in textual form as an (X)HTML table, and may be saved as parsable plain text or XML.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK. d.leader@bio.gla.ac.uk

ABSTRACT

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 alphabeta-motifs, asx-motifs, asx-turns, beta-bulges, beta-bulge loops, beta-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.

Show MeSH