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  Protein sequence analysis using the MPI Bioinformatics Toolkit

Gabler, F., Nam, S.-Z., Till, S., Mirdita, M., Steinegger, M., Söding, J., et al. (2020). Protein sequence analysis using the MPI Bioinformatics Toolkit. Current Protocols in Bioinformatics, 72(1): e108. doi:10.1002/cpbi.108.

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 Creators:
Gabler, F., Author
Nam, S.-Z., Author
Till, S., Author
Mirdita, M.1, Author              
Steinegger, M.1, Author              
Söding, J.1, Author              
Lupas, A. N., Author
Alva, V., Author
Affiliations:
1Research Group of Computational Biology, MPI for Biophysical Chemistry, Max Planck Society, ou_1933286              

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Free keywords: CLANS; cluster analysis; HHpred; HMM; homology; profile hidden Markov models; sequence comparison; sequence similarity searches; structure prediction
 Abstract: The MPI Bioinformatics Toolkit (https://toolkit.tuebingen.mpg.de) provides interactive access to a wide range of the best‐performing bioinformatics tools and databases, including the state‐of‐the‐art protein sequence comparison methods HHblits and HHpred. The Toolkit currently includes 35 external and in‐house tools, covering functionalities such as sequence similarity searching, prediction of sequence features, and sequence classification. Due to this breadth of functionality, the tight interconnection of its constituent tools, and its ease of use, the Toolkit has become an important resource for biomedical research and for teaching protein sequence analysis to students in the life sciences. In this article, we provide detailed information on utilizing the three most widely accessed tools within the Toolkit: HHpred for the detection of homologs, HHpred in conjunction with MODELLER for structure prediction and homology modeling, and CLANS for the visualization of relationships in large sequence datasets. Basic Protocol 1: Sequence similarity searching using HHpred Alternate Protocol: Pairwise sequence comparison using HHpred Support Protocol: Building a custom multiple sequence alignment using PSI‐BLAST and forwarding it as input to HHpred Basic Protocol 2: Calculation of homology models using HHpred and MODELLER Basic Protocol 3: Cluster analysis using CLANS

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Language(s): eng - English
 Dates: 2020-12-14
 Publication Status: Published online
 Pages: -
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 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1002/cpbi.108
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Title: Current Protocols in Bioinformatics
Source Genre: Journal
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Pages: 30 Volume / Issue: 72 (1) Sequence Number: e108 Start / End Page: - Identifier: -