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Open Access Software

Defining and searching for structural motifs using DeepView/Swiss-PdbViewer

Maria U Johansson1, Vincent Zoete2, Olivier Michielin2 and Nicolas Guex1*

Author Affiliations

1 Vital-IT Group, SIB Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland

2 Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland

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BMC Bioinformatics 2012, 13:173  doi:10.1186/1471-2105-13-173

Published: 23 July 2012

Abstract

Background

Today, recognition and classification of sequence motifs and protein folds is a mature field, thanks to the availability of numerous comprehensive and easy to use software packages and web-based services. Recognition of structural motifs, by comparison, is less well developed and much less frequently used, possibly due to a lack of easily accessible and easy to use software.

Results

In this paper, we describe an extension of DeepView/Swiss-PdbViewer through which structural motifs may be defined and searched for in large protein structure databases, and we show that common structural motifs involved in stabilizing protein folds are present in evolutionarily and structurally unrelated proteins, also in deeply buried locations which are not obviously related to protein function.

Conclusions

The possibility to define custom motifs and search for their occurrence in other proteins permits the identification of recurrent arrangements of residues that could have structural implications. The possibility to do so without having to maintain a complex software/hardware installation on site brings this technology to experts and non-experts alike.