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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Motivated proteins: a web application for studying small three-dimensional protein motifs
David P Leader1, E James Milner-White
1Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK. d.leader@bio.gla.ac.uk
BMC Bioinformatics
|February 13, 2009
Summary
Scientists can now explore small protein motifs using the Motivated Proteins web application. This tool provides access to a database of 12 common protein motifs, aiding structural biology research.
Area of Science:
- Structural Biology
- Bioinformatics
Background:
- Small loop-shaped motifs are integral to protein 3D structure, typically consisting of 3-7 amino acids.
- Common motifs include alphabeta-motifs, asx-motifs, beta-turns, and Schellmann loops, defined by dihedral angles and hydrogen bonding.
- A comprehensive database of these motifs was compiled from high-quality protein structures.
Purpose of the Study:
- To develop a user-friendly web application for visualizing and analyzing small protein motifs.
- To provide researchers with easy access to a curated database of protein structural motifs.
Main Methods:
- A web application, Motivated Proteins, was created to interface with a database of 12 motif types (48 sub-categories) across over 400 proteins.
- Query functionalities include searching for specific motifs, motifs near ligands or active sites, overlapping motifs, or motifs with particular sequences.
- Results are presented in HTML tables, with options for plain text or XML export, and visualized using the Jmol applet.
Main Results:
- The Motivated Proteins application offers access to a diverse range of protein motifs and their structural contexts.
- Users can perform complex queries and visualize motifs individually or within their protein structure.
- Detailed information, including amino acid distributions and dihedral angle graphs, is available for each motif.
Conclusions:
- Motivated Proteins is a free, publicly accessible web tool for studying protein motifs.
- It empowers protein scientists to analyze 3D structural motifs without needing database query language expertise.
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