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The MULTICOM toolbox for protein structure prediction

Jianlin Cheng123*, Jilong Li1, Zheng Wang1, Jesse Eickholt1 and Xin Deng1

Author Affiliations

1 Department of Computer Science, University of Missouri-Columbia, Columbia, MO, 65211, USA

2 Informatics Institute, University of Missouri-Columbia, Columbia, MO, 65211, USA

3 C. Bond Life Science Center, University of Missouri-Columbia, Columbia, MO, 65211, USA

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BMC Bioinformatics 2012, 13:65  doi:10.1186/1471-2105-13-65

Published: 30 April 2012

Abstract

Background

As genome sequencing is becoming routine in biomedical research, the total number of protein sequences is increasing exponentially, recently reaching over 108 million. However, only a tiny portion of these proteins (i.e. ~75,000 or < 0.07%) have solved tertiary structures determined by experimental techniques. The gap between protein sequence and structure continues to enlarge rapidly as the throughput of genome sequencing techniques is much higher than that of protein structure determination techniques. Computational software tools for predicting protein structure and structural features from protein sequences are crucial to make use of this vast repository of protein resources.

Results

To meet the need, we have developed a comprehensive MULTICOM toolbox consisting of a set of protein structure and structural feature prediction tools. These tools include secondary structure prediction, solvent accessibility prediction, disorder region prediction, domain boundary prediction, contact map prediction, disulfide bond prediction, beta-sheet topology prediction, fold recognition, multiple template combination and alignment, template-based tertiary structure modeling, protein model quality assessment, and mutation stability prediction.

Conclusions

These tools have been rigorously tested by many users in the last several years and/or during the last three rounds of the Critical Assessment of Techniques for Protein Structure Prediction (CASP7-9) from 2006 to 2010, achieving state-of-the-art or near performance. In order to facilitate bioinformatics research and technological development in the field, we have made the MULTICOM toolbox freely available as web services and/or software packages for academic use and scientific research. It is available at http://sysbio.rnet.missouri.edu/multicom_toolbox/ webcite.

Keywords:
Protein structure prediction; Bioinformatics tool; Secondary structure; Solvent accessibility; Domain; Contact map; Tertiary structure; Protein model quality assessment; Fold recognition; Protein disorder