Söding Johannes, Biegert Andreas, Lupas Andrei N
Department of Protein Evolution, Max-Planck-Institute for Developmental Biology Spemannstrasse 35, 72076 Tübingen, Germany.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W244-8. doi: 10.1093/nar/gki408.
HHpred is a fast server for remote protein homology detection and structure prediction and is the first to implement pairwise comparison of profile hidden Markov models (HMMs). It allows to search a wide choice of databases, such as the PDB, SCOP, Pfam, SMART, COGs and CDD. It accepts a single query sequence or a multiple alignment as input. Within only a few minutes it returns the search results in a user-friendly format similar to that of PSI-BLAST. Search options include local or global alignment and scoring secondary structure similarity. HHpred can produce pairwise query-template alignments, multiple alignments of the query with a set of templates selected from the search results, as well as 3D structural models that are calculated by the MODELLER software from these alignments. A detailed help facility is available. As a demonstration, we analyze the sequence of SpoVT, a transcriptional regulator from Bacillus subtilis. HHpred can be accessed at http://protevo.eb.tuebingen.mpg.de/hhpred.
HHpred是一个用于远程蛋白质同源性检测和结构预测的快速服务器，并且是首个实现轮廓隐马尔可夫模型（HMM）成对比较的工具。它允许搜索多种数据库，如蛋白质数据银行（PDB）、蛋白质结构分类（SCOP）、蛋白质家族数据库（Pfam）、简单模块构架搜索工具（SMART）、直系同源簇（COGs）和保守结构域数据库（CDD）。它接受单个查询序列或多序列比对作为输入。在短短几分钟内，它就能以类似于位置特异性迭代比对搜索工具（PSI-BLAST）的用户友好格式返回搜索结果。搜索选项包括局部或全局比对以及对二级结构相似性进行评分。HHpred可以生成查询序列与模板的成对比对、查询序列与从搜索结果中选择的一组模板的多序列比对，以及由MODELLER软件根据这些比对计算出的三维结构模型。有详细的帮助工具可供使用。作为示例，我们分析了枯草芽孢杆菌转录调节因子SpoVT的序列。可通过http://protevo.eb.tuebingen.mpg.de/hhpred访问HHpred。
