Zhou Fengfeng, Xue Yu, Yao Xuebiao, Xu Ying
Computational Systems Biology Laboratory, Department of Biochemical and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, USA.
Nat Protoc. 2006;1(3):1318-21. doi: 10.1038/nprot.2006.209.
Post-translational modifications (PTMs) of proteins play essential roles in governing the functions and dynamics of proteins and are implicated in many cellular processes. Several types of PTMs have been investigated through computational approaches, including phosphorylation, sumoylation, palmitoylation, and lysine and arginine methylation, among others. Because the large diversity in the user interfaces (UIs) of different prediction servers for PTMs could possibly hinder experimental biologists in using these servers, we propose to develop a protocol for a unified UI for PTM prediction servers, based on our own work and that of other groups on PTM site prediction. By following this protocol, tool developers can provide a uniform UI regardless of the PTM types and the underlying computational algorithms. With such uniformity in the UI, experimental biologists would be able to use any PTM prediction server compliant with this protocol once they had learned to use one of them. It takes a typical PTM prediction server compliant with this unified UI several minutes to calculate the prediction results for a protein 1,000 amino acids in length.
蛋白质的翻译后修饰（PTM）在调控蛋白质的功能和动态变化中起着至关重要的作用，并涉及许多细胞过程。已经通过计算方法研究了几种类型的PTM，包括磷酸化、SUMO化、棕榈酰化以及赖氨酸和精氨酸甲基化等。由于不同PTM预测服务器的用户界面（UI）存在很大差异，这可能会阻碍实验生物学家使用这些服务器，因此我们建议基于我们自己以及其他团队在PTM位点预测方面的工作，开发一种用于PTM预测服务器统一UI的协议。遵循此协议，工具开发者可以提供统一的UI，而不管PTM类型和底层计算算法如何。有了这样统一的UI，实验生物学家一旦学会使用其中一个符合该协议的PTM预测服务器，就能够使用任何其他符合该协议的服务器。一个符合这种统一UI的典型PTM预测服务器计算一个长度为1000个氨基酸的蛋白质的预测结果需要几分钟时间。
