CMWeb: an interactive on-line tool for analysing residue-residue contacts and contact prediction methods
CMWeb: an interactive on-line tool for analysing residue-residue contacts and contact prediction methods
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DOI：
10.1093/nar/gks488
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发表时间：
2012-07-01
影响因子：
14.9
通讯作者：
Tusnady, Gabor E.
中科院分区：
文献类型：
--
作者：
Kozma, Daniel;Simon, Istvan;Tusnady, Gabor E.
接触图是蛋白质三维结构的2D衍生，包含结构中各种残基-残基(RR)接触。接触图可以用于高精度的结构重建，并且可以根据氨基酸序列进行预测。因此，了解接触图的各种性质是蛋白质结构预测的重要一步。为了研究联系人形成和联系人集群的基本属性，我们建立了一个集成系统，称为联系人地图Web查看器，简称CMWeb。该服务器可用于可视化联系人地图、链接联系人并以3D结构和多序列比对显示它们，以及计算关于联系人的各种统计数据。此外，我们在CMWeb服务器上实现了五种联系人预测方法，将预测的RR联系人和真实的RR联系人可视化在一个联系人地图中。其他RR接触预测方法的结果也可以作为基准测试上传到服务器上。所有这些功能都在Web服务器后面，因此，要使用我们的应用程序，只需要一个支持Java的Web浏览器，不需要进一步的程序安装。CMWEB可在http://cmweb.enzim.hu.上免费访问
A contact map is a 2D derivative of the 3D structure of proteins, containing various residue-residue (RR) contacts within the structure. Contact maps can be used for the reconstruction of structure with high accuracy and can be predicted from the amino acid sequence. Therefore understanding the various properties of contact maps is an important step in protein structure prediction. For investigating basic properties of contact formation and contact clusters we set up an integrated system called Contact Map Web Viewer, or CMWeb for short. The server can be used to visualize contact maps, to link contacts and to show them both in 3D structures and in multiple sequence alignments and to calculate various statistics on contacts. Moreover, we have implemented five contact prediction methods in the CMWeb server to visualize the predicted and real RR contacts in one contact map. The results of other RR contact prediction methods can be uploaded as a benchmark test onto the server as well. All of these functionality is behind a web server, thus for using our application only a Java-capable web browser is needed, no further program installation is required. The CMWeb is freely accessible at http://cmweb.enzim.hu.