National Institute of Biomedical Innovation, 7-6-8, Saito-asagi, Ibaraki, Osaka 5670085, Japan.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W398-401. doi: 10.1093/nar/gkq360. Epub 2010 May 10.
Conserved residues forming tightly packed clusters have been shown to be energy hot spots in both protein-protein and protein-DNA complexes. A number of analyses on these clusters of conserved residues (CCRs) have been reported, all pointing to a crucial role that these clusters play in protein function, especially protein-protein and protein-DNA interactions. However, currently there is no publicly available tool to automatically detect such clusters. Here, we present a web server that takes a coordinate file in PDB format as input and automatically executes all the steps to identify CCRs in protein structures. In addition, it calculates the structural properties of each residue and of the CCRs. We also present statistics to show that CCRs, determined by these procedures, are significantly enriched in 'hot spots' in protein-protein and protein-RNA complexes, which supplements our more detailed similar results on protein-DNA complexes. We expect that CCRXP web server will be useful in studies of protein structures and their interactions and selecting mutagenesis targets. The web server can be accessed at http://ccrxp.netasa.org.
已证明，在蛋白质-蛋白质和蛋白质-DNA 复合物中，形成紧密堆积簇的保守残基是能量热点。已经有许多关于这些保守残基簇 (CCR) 的分析报告，所有这些报告都指出这些簇在蛋白质功能中起着关键作用，特别是在蛋白质-蛋白质和蛋白质-DNA 相互作用中。然而，目前还没有公共可用的工具可以自动检测这些簇。在这里，我们提供了一个网络服务器，它以 PDB 格式的坐标文件作为输入，并自动执行所有步骤来识别蛋白质结构中的 CCR。此外，它还计算了每个残基和 CCR 的结构特性。我们还提供了统计数据，表明通过这些程序确定的 CCR 在蛋白质-蛋白质和蛋白质-RNA 复合物的“热点”中明显富集，这补充了我们在蛋白质-DNA 复合物上更详细的类似结果。我们希望 CCRXP 网络服务器在研究蛋白质结构及其相互作用和选择诱变靶标时将是有用的。该网络服务器可在 http://ccrxp.netasa.org 访问。
