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Bioinformatics Tool Development

The development of bioinformatics tools is an essential part of molecular biological research and the focus of our work. In order to empower experimental scientists, we have developed the MPI Bioinformatics Toolkit, which integrates state-of-the-art software for protein sequence and structure analysis into an intuitively usable platform [1]. At this time our toolkit consists of 55 applications, most of which are interconnected, allowing job results to be forwarded between applications.

Around half of the tools available were developed in-house. One of our most important developments has been to harness pairwise hidden Markov model (HMM) comparisons for sequence analysis and structure prediction [2]. With HHsearch, which is employed by our server HHpred [3] and by many others of our tools, we were the first to offer a fast and reliable algorithm for remote homology detection through HMM-HMM comparison. We also developed a protein classification tool, CLANS [4], which uses a  variant of the Fruchterman-Reingold graph layout algorithm to analyze relationships in large sequence datasets. HHpred and CLANS are at the core of many of our papers [e.g. 5-8].

In addition to in-house developments, we have also integrated several public tools into our platform, some of which are offered as customized versions with extended functionality. We continuously strive to develop and integrate new tools into the toolkit and to improve its accessibility and user-friendliness.

References

[1] Biegert A., Mayer C., Remmert M., Söding J., Lupas AN. (2006) The MPI Bioinformatics Toolkit for Protein Sequence Analysis.
Nucl Acid Res 34(Web Server Issue) W335-339
PMID: 16845021
 
[2] Söding J. (2004) Protein homology detection by HMM-HMM comparison. Bioinformatics 21(7): 951-960
PMID: 15531603
 
[3] Söding J., Biegert A., Lupas AN. (2005) The HHpred interactive server for protein homology detection and structure prediction.
Nucl Acid Res 33(Web Server Issue) W244-248
PMID: 15980461
 
[4] Frickey T., Lupas A. (2004) CLANS: a Java application for visualizing protein families based on pairwise similarity.
Bioinformatics 20(18): 3702-04
PMID: 15284097
 
[5] Ammelburg M., Frickey T., Lupas AN. (2006) Classification of AAA+ proteins. J Struct Biol 156(1):2-11
PMID: 16828312
 
[6] Alva V., Ammelburg M., Söding J., Lupas AN. (2007) On the origin of the histone fold. BMC Struct Biol 7:17
PMID: 17391511
 
[7] Kopec KO., Alva V., Lupas AN. (2010) Homology of SMP domains to the TULIP superfamily of lipid-binding proteins provides a
structural basis for lipid exchange between ER and mitochondria. 
Bioinformatics 26(16):1927-31
PMID: 20554689
 
[8] Dunin-Horkawicz S., Kopec KO., Lupas AN. (2014) Prokaryotic ancestry of eukaryotic protein networks mediating innate immunity
and apoptosis. 
J Mol Biol 426(7):1568-82
PMID: 24333018