Prism: Protein-Protein Interaction Prediction by Structural Matching
Prism: Protein-Protein Interaction Prediction by Structural Matching
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DOI：
10.1007/978-1-59745-398-1_30
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发表时间：
2008-01-01
期刊：
影响因子：
--
通讯作者：
Gursoy, Attila
中科院分区：
文献类型：
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作者：
Keskin, Ozlem;Nussinov, Ruth;Gursoy, Attila
棱镜（结构匹配的蛋白质相互作用）是一种采用新型预测算法来实现蛋白质 - 蛋白质相互作用的系统。它采用了一种自下而上的方法，该方法结合了蛋白质界面中的结构和序列保护。该算法通过结构相似性和已知界面的进化保护寻求蛋白质之间可能的二元相互作用。它由包含蛋白质数据库（PDB）和预测蛋白质蛋白质相互作用的蛋白质界面结构的数据库组成。它还提供有关蛋白质和交互式蛋白接口查看器的相关信息。在当前版本中，3799结构非冗余界面轮胎用于预测6170蛋白之间的相互作用。在两个公开可用的交互数据库（DIP和BIND）中验证了大量相互作用。由于经过验证的相互作用证明了我们方法的适用性，因此未经验证的相互作用可能指出了未发现的相互作用。可以通过用户友好的网站（http://prism.ccbb.ku.edu.tr）访问Prism，并且随着新蛋白质结构在PDB中可用时，它将定期更新。用户可以浏览预测算法所依赖的代表性接口的非冗余数据集，检索类似于这些接口的结构列表，或者查看特定蛋白质的交互预测结果。提供的另一项服务是交互式预测。这是通过运行用户输入结构的算法来完成的。
Prism (protein interactions by structural matching) is a system that employs a novel prediction algorithm for protein-protein interactions. It adopts a bottom-up approach that combines structure and sequence conservation in protein interfaces. The algorithm seeks possible binary interactions between proteins through structure similarity and evolutionary conservation of known interfaces. It is composed of a database containing protein interface Structures derived from the Protein Data Bank (PDB) and predicted protein-protein interactions. It also provides related information about the proteins and in interactive protein interface viewer. In the current version, 3799 structurally nonredundant interfaces tire used to predict the interactions among 6170 proteins. A substantial number of interactions are verified in two publicly available interaction databases (DIP and BIND). As the verified interactions demonstrate the Suitability of our approach, unverified ones may point to undiscovered interactions. Prism can be accessed through a user-friendly website (http://prism.ccbb.ku.edu.tr) and it will be updated regularly as new protein structures become available in the PDB. Users may browse through the nonredundant dataset of representative interfaces on which the prediction algorithm depends, retrieve the list of structures similar to these interfaces, or see the results of interaction predictions for a particular protein. Another service provided is the interactive prediction. This is done by running the algorithm for the user input structures.