Structure Motivator: A tool for exploring small three-dimensional elements in proteins

BMC Structural Biology

E James Milner-White¹  David P Leader¹ 

[1]College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK

关键词: Relational database;    Dihedral angle;    Ramachandran plot;    Protein motif;   

Others  :  1091793
DOI  :  10.1186/1472-6807-12-26

 received in 2012-06-19, accepted in 2012-10-12,  发布年份 2012

【 摘 要 】

Background

Protein structures incorporate characteristic three-dimensional elements defined by some or all of hydrogen bonding, dihedral angles and amino acid sequence. The software application, Structure Motivator, allows interactive exploration and analysis of such elements, and their resolution into sub-classes.

Results

Structure Motivator is a standalone application with an embedded relational database of proteins that, as a starting point, can furnish the user with a palette of unclassified small peptides or a choice of pre-classified structural motifs. Alternatively the application accepts files of data generated externally. After loading, the structural elements are displayed as two-dimensional plots of dihedral angles (φ/ψ, φ/χ1 or in combination) for each residue, with visualization options to allow the conformation or amino acid composition at one residue to be viewed in the context of that at other residues. Interactive selections may then be made and structural subsets saved to file for further sub-classification or external analysis. The application has been applied both to classical motifs, such as the β-turn, and ‘non-motif’ structural elements, such as specific segments of helices.

Conclusions

Structure Motivator allows structural biologists, whether or not they possess computational skills, to subject small structural elements in proteins to rapid interactive analysis that would otherwise require complex programming or database queries. Within a broad group of structural motifs, it facilitates the identification and separation of sub-classes with distinct stereochemical properties.

【 授权许可】

   
2012 Leader and Milner-White; licensee BioMed Central Ltd.

【 图 表 】

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