ProMateus--an open research approach to protein-binding sites analysis.
ProMateus--an open research approach to protein-binding sites analysis.
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DOI：
10.1093/nar/gkm301
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发表时间：
2007-07
影响因子：
14.9
通讯作者：
Schreiber, Gideon
中科院分区：
文献类型：
--
作者：
Neuvirth, Hani;Heinemann, Uri;Birnbaum, David;Tishby, Naftali;Schreiber, Gideon
各个实验室开发的生物信息学工具导致了相同任务的大量并行程序。例如，使用ProMate、WHISCY、PPI-Pred、PINUP等进行相互作用蛋白质之间的结合位点区域的鉴定。所有服务器首先识别绑定站点的独特属性，然后将它们合并到预测器中。显然，如果将来自这些预测器中的每一个的最合适的参数合并到一个服务器中，则所得到的预测将得到改善。然而，由于方法和数据库的差异，目前尚不可行。在这里，蛋白质结合位点预测服务器扩展成一个通用的蛋白质结合位点研究工具，ProMateus。这一网络工具以ProMate的基础设施为基础，使用户能够方便地探索和纳入新的功能和数据库，在一套框架内对个别功能及其组合的好处进行评估。这将个人研究转变为社区练习，从所有用户中获得最佳预测。该分析证明了蛋白质和蛋白质-DNA相互作用的数据库。这种方法与生成元服务器的方法基本不同。开放式研究方法的影响进行了讨论。ProMateus可在www.example.com上获得。
The development of bioinformatic tools by individual labs results in the abundance of parallel programs for the same task. For example, identification of binding site regions between interacting proteins is done using: ProMate, WHISCY, PPI-Pred, PINUP and others. All servers first identify unique properties of binding sites and then incorporate them into a predictor. Obviously, the resulting prediction would improve if the most suitable parameters from each of those predictors would be incorporated into one server. However, because of the variation in methods and databases, this is currently not feasible. Here, the protein-binding site prediction server is extended into a general protein-binding sites research tool, ProMateus. This web tool, based on ProMate's infrastructure enables the easy exploration and incorporation of new features and databases by the user, providing an evaluation of the benefit of individual features and their combination within a set framework. This transforms the individual research into a community exercise, bringing out the best from all users for optimized predictions. The analysis is demonstrated on a database of protein protein and protein-DNA interactions. This approach is basically different from that used in generating meta-servers. The implications of the open-research approach are discussed. ProMateus is available at http://bip.weizmann.ac.il/promate.