Sequence searches are a common first step in this process, as sequence similarity is widely accepted as the best marker for substantiating homologous relationships.
The structure, function, and evolution of new or uncharacterized proteins are routinely inferred based on their homology to proteins with experimentally characterized properties. Support Protocol: Building a custom multiple sequence alignment using PSI-BLAST and forwarding it as input to HHpredīasic Protocol 2: Calculation of homology models using HHpred and MODELLERīasic Protocol 3: Cluster analysis using CLANS © 2020 The Authors.īasic Protocol 1: Sequence similarity searching using HHpredĪlternate Protocol: Pairwise sequence comparison using HHpred 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. 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. The Toolkit currently includes 35 external and in-house tools, covering functionalities such as sequence similarity searching, prediction of sequence features, and sequence classification. The MPI Bioinformatics Toolkit ( ) 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.
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