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

By Vikram Alva, Seung-Zin Nam, Johannes Söding, Andrei N. Lupas. 2016

375 citations recorded by the source corpus.

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.

Subfields: Ecology, Materials Chemistry, Molecular Biology

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Citations in the corpus

Protein Sequence Analysis Using the MPI Bioinformatics Toolkit (2020, methodology): “The Toolkit has been in continuous operation ever since, and we replaced the first version with an entirely new one built using more scalable and robust web technologies in 2017 (Alva, Nam, Soding, & Lupas, 2016; Zimmermann et al., 2018).”
The Centrosome Is a Selective Condensate that Nucleates Microtubules by Concentrating Tubulin. (2017, background): “Domain organization of SPD-5 showing coiled-coil domains (top, analysis with MARCOIL at 90% threshold (Alva et al., 2016)) and disordered regions (bottom, analysis with PONDR-FIT (Xue et al., 2010)).”
Systematic discovery of anti-phage defense systems in the microbial pan-genome (2018, methodology): “J. Söding, A. Biegert, A. N. Lupas, The HHpred interactive server for protein homology detection and structure prediction.”
Enhancing structure prediction and design of soluble and membrane proteins with explicit solvent-protein interactions (2017, methodology): “As a comparison to SPaDES implemented into the homology modeling protocol of RosettaMembrane, the sequence alignments and template structures from the benchmark described in the Homology modeling of GPCRs section were input into Modeller while all other input options were kept as the defaults set in”