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. 2016 Jul 8;44(W1):W410-5.
doi: 10.1093/nar/gkw348. Epub 2016 Apr 29.

The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis

Vikram Alva  1 , Seung-Zin Nam  2 , Johannes Söding  3 , Andrei N Lupas  4
Affiliations

The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis

Vikram Alva et al. Nucleic Acids Res. .

Abstract

The MPI Bioinformatics Toolkit (http://toolkit.tuebingen.mpg.de) is an open, interactive web service for comprehensive and collaborative protein bioinformatic analysis. It offers a wide array of interconnected, state-of-the-art bioinformatics tools to experts and non-experts alike, developed both externally (e.g. BLAST+, HMMER3, MUSCLE) and internally (e.g. HHpred, HHblits, PCOILS). While a beta version of the Toolkit was released 10 years ago, the current production-level release has been available since 2008 and has serviced more than 1.6 million external user queries. The usage of the Toolkit has continued to increase linearly over the years, reaching more than 400 000 queries in 2015. In fact, through the breadth of its tools and their tight interconnection, the Toolkit has become an excellent platform for experimental scientists as well as a useful resource for teaching bioinformatic inquiry to students in the life sciences. In this article, we report on the evolution of the Toolkit over the last ten years, focusing on the expansion of the tool repertoire (e.g. CS-BLAST, HHblits) and on infrastructural work needed to remain operative in a changing web environment.

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Figures

Figure 1.
Figure 1.
Toolkit usage and citations. The number of queries from external IP addresses in thousands is shown by the blue line and the citations of the Toolkit framework and the tools developed by us, as indicated by Google Scholar, is shown by the green line.
Figure 2.
Figure 2.
Interconnection of the tools in the Toolkit. The output of most tools can be forwarded as input to many other tools. One such possible forwarding pipeline is shown, wherein the output of the sensitive search method CS-BLAST is forwarded to Blammer to parse out a multiple alignment, which is subsequently forwarded to Quick2D for secondary structure prediction and HHpred for the identification of remote homologs. The output of HHpred is then forwarded to Modeller in order to obtain a structural model.
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