SA-Search：一种基于结构字母表的蛋白质结构挖掘网络工具。
SA-Search: a web tool for protein structure mining based on a Structural Alphabet.
作者信息
Guyon Frédéric, Camproux Anne-Claude, Hochez Joëlle, Tufféry Pierre
机构信息
Equipe de Bioinformatique Génomique et Moléculaire, INSERM E346, Université Paris 7, Case 7113, 2 Place Jussieu, 75251 Paris cedex 05, France.
出版信息
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W545-8. doi: 10.1093/nar/gkh467.
Abstract
SA-Search is a web tool that can be used to mine for protein structures and extract structural similarities. It is based on a hidden Markov model derived Structural Alphabet (SA) that allows the compression of three-dimensional (3D) protein conformations into a one-dimensional (1D) representation using a limited number of prototype conformations. Using such a representation, classical methods developed for amino acid sequences can be employed. Currently, SA-Search permits the performance of fast 3D similarity searches such as the extraction of exact words using a suffix tree approach, and the search for fuzzy words viewed as a simple 1D sequence alignment problem. SA-Search is available at http://bioserv.rpbs.jussieu.fr/cgi-bin/SA-Search.
摘要
SA-Search是一种网络工具，可用于挖掘蛋白质结构并提取结构相似性。它基于一种源自结构字母表（SA）的隐马尔可夫模型，该模型允许使用有限数量的原型构象将三维（3D）蛋白质构象压缩为一维（1D）表示形式。使用这种表示形式，可以采用为氨基酸序列开发的经典方法。目前，SA-Search允许执行快速的3D相似性搜索，例如使用后缀树方法提取精确词，以及将模糊词搜索视为简单的一维序列比对问题。可通过http://bioserv.rpbs.jussieu.fr/cgi-bin/SA-Search访问SA-Search。
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