Protein Sequence Analysis Using the MPI Bioinformatics Toolkit.
Protein Sequence Analysis Using the MPI Bioinformatics Toolkit.
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DOI：
10.1002/cpbi.108
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发表时间：
2020-12-01
影响因子：
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通讯作者：
Alva, Vikram
中科院分区：
文献类型：
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作者：
Gabler, Felix;Nam, Seung-Zin;Alva, Vikram
MPI Bioinformatics Toolkit（https：toolkit.tuebingen.mpg.de）提供了对各种最佳生物信息学工具和数据库的交互式访问，包括最先进的蛋白质序列比较方法HHblits和HHpred。该工具包目前包括35个外部和内部工具，涵盖序列相似性搜索、序列特征预测和序列分类等功能。由于其广泛的功能，其组成工具的紧密互连以及易于使用，该工具包已成为生物医学研究和教授生命科学学生蛋白质序列分析的重要资源。在这篇文章中，我们提供了有关利用工具包中三个最广泛访问的工具的详细信息：HHpred用于同源物检测，HHpred与MODELLER结合用于结构预测和同源性建模，以及CLANS用于大型序列数据集中关系的可视化。版权所有2020作者。基本方案1：使用HHpred的序列相似性搜索替代方案：使用HHpred的成对序列比较支持方案：使用PSI-BLAST构建定制的多序列比对并将其作为输入转发到HHpred基本方案2：使用HHpred和MODELLER基本方案3计算同源性模型：使用CLANS进行聚类分析。
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. © 2020 The Authors. 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.