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Open Access Methodology article

ConSole: using modularity of Contact maps to locate Solenoid domains in protein structures

Thomas Hrabe and Adam Godzik*

Author Affiliations

Program in Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, 92037 La Jolla, CA, USA

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BMC Bioinformatics 2014, 15:119  doi:10.1186/1471-2105-15-119

Published: 27 April 2014

Abstract

Background

Periodic proteins, characterized by the presence of multiple repeats of short motifs, form an interesting and seldom-studied group. Due to often extreme divergence in sequence, detection and analysis of such motifs is performed more reliably on the structural level. Yet, few algorithms have been developed for the detection and analysis of structures of periodic proteins.

Results

ConSole recognizes modularity in protein contact maps, allowing for precise identification of repeats in solenoid protein structures, an important subgroup of periodic proteins. Tests on benchmarks show that ConSole has higher recognition accuracy as compared to Raphael, the only other publicly available solenoid structure detection tool. As a next step of ConSole analysis, we show how detection of solenoid repeats in structures can be used to improve sequence recognition of these motifs and to detect subtle irregularities of repeat lengths in three solenoid protein families.

Conclusions

The ConSole algorithm provides a fast and accurate tool to recognize solenoid protein structures as a whole and to identify individual solenoid repeat units from a structure. ConSole is available as a web-based, interactive server and is available for download at http://console.sanfordburnham.org webcite.

Keywords:
Protein repeat detection; Solenoid structure; Contact map; Template matching; Machine learning