Nimrod Guy, Schushan Maya, Steinberg David M, Ben-Tal Nir
Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel.
Structure. 2008 Dec 10;16(12):1755-63. doi: 10.1016/j.str.2008.10.017.
Structural genomics initiatives provide ample structures of "hypothetical proteins" (i.e., proteins of unknown function) at an ever increasing rate. However, without function annotation, this structural goldmine is of little use to biologists who are interested in particular molecular systems. To this end, we used (an improved version of) the PatchFinder algorithm for the detection of functional regions on the protein surface, which could mediate its interactions with, e.g., substrates, ligands, and other proteins. Examination, using a data set of annotated proteins, showed that PatchFinder outperforms similar methods. We collected 757 structures of hypothetical proteins and their predicted functional regions in the N-Func database. Inspection of several of these regions demonstrated that they are useful for function prediction. For example, we suggested an interprotein interface and a putative nucleotide-binding site. A web-server implementation of PatchFinder and the N-Func database are available at http://patchfinder.tau.ac.il/.
结构基因组学计划正以越来越快的速度提供大量“假设性蛋白质”（即功能未知的蛋白质）的结构。然而，若没有功能注释，这座结构宝库对于关注特定分子系统的生物学家来说用处不大。为此，我们使用了PatchFinder算法（改进版）来检测蛋白质表面的功能区域，这些区域可能介导其与底物、配体及其他蛋白质等的相互作用。使用一组注释蛋白质数据集进行的检验表明，PatchFinder优于类似方法。我们在N-Func数据库中收集了757个假设性蛋白质的结构及其预测的功能区域。对其中几个区域的检查表明，它们对功能预测很有用。例如，我们提出了一个蛋白质间界面和一个假定的核苷酸结合位点。可通过http://patchfinder.tau.ac.il/访问PatchFinder的网络服务器版本和N-Func数据库。
