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J Mol Biol. 2018 Jul 20;430(15):2237-2243. doi: 10.1016/j.jmb.2017.12.007. Epub 2017 Dec 16.

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core.

Author information

1
Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen D-72076, Germany.
2
Group for Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Göttingen D-37077, Germany.
3
Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen D-72076, Germany. Electronic address: andrei.lupas@tuebingen.mpg.de.
4
Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen D-72076, Germany. Electronic address: vikram.alva@tuebingen.mpg.de.

Abstract

The MPI Bioinformatics Toolkit (https://toolkit.tuebingen.mpg.de) is a free, one-stop web service for protein bioinformatic analysis. It currently offers 34 interconnected external and in-house tools, whose functionality covers sequence similarity searching, alignment construction, detection of sequence features, structure prediction, and sequence classification. This breadth has made the Toolkit an important resource for experimental biology and for teaching bioinformatic inquiry. Recently, we replaced the first version of the Toolkit, which was released in 2005 and had served around 2.5 million queries, with an entirely new version, focusing on improved features for the comprehensive analysis of proteins, as well as on promoting teaching. For instance, our popular remote homology detection server, HHpred, now allows pairwise comparison of two sequences or alignments and offers additional profile HMMs for several model organisms and domain databases. Here, we introduce the new version of our Toolkit and its application to the analysis of proteins.

KEYWORDS:

HHblits; HHpred; MPI Bioinformatics Toolkit; remote homology detection; structure prediction

PMID:
29258817
DOI:
10.1016/j.jmb.2017.12.007

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