![]() The Toolkit currently includes 35 in-house and external tools for sequence similarity searching calculation of multiple sequence alignments prediction of secondary structure and sequence features and sequence classification. 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). ![]() Driven by our work at the interface of computational and experimental biology, we launched the MPI Bioinformatics Toolkit in 2005 to provide researchers in the life sciences with easy, web-based access to the best-performing bioinformatics tools and databases (Biegert, Mayer, Remmert, Soding, & Lupas, 2006). Over the years, many high-quality sequence search methods protein sequence and domain databases and integrative Web resources have been developed to help researchers make meaningful inferences based on homology. 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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