Chou Kuo-Chen, Shen Hong-Bin
Gordon Life Science Institute, 13784 Torrey Del Mar Drive, San Diego, California 92130, USA.
Nat Protoc. 2008;3(2):153-62. doi: 10.1038/nprot.2007.494.
Information on subcellular localization of proteins is important to molecular cell biology, proteomics, system biology and drug discovery. To provide the vast majority of experimental scientists with a user-friendly tool in these areas, we present a package of Web servers developed recently by hybridizing the 'higher level' approach with the ab initio approach. The package is called Cell-PLoc and contains the following six predictors: Euk-mPLoc, Hum-mPLoc, Plant-PLoc, Gpos-PLoc, Gneg-PLoc and Virus-PLoc, specialized for eukaryotic, human, plant, Gram-positive bacterial, Gram-negative bacterial and viral proteins, respectively. Using these Web servers, one can easily get the desired prediction results with a high expected accuracy, as demonstrated by a series of cross-validation tests on the benchmark data sets that covered up to 22 subcellular location sites and in which none of the proteins included had > or =25% sequence identity to any other protein in the same subcellular-location subset. Some of these Web servers can be particularly used to deal with multiplex proteins as well, which may simultaneously exist at, or move between, two or more different subcellular locations. Proteins with multiple locations or dynamic features of this kind are particularly interesting, because they may have some special biological functions intriguing to investigators in both basic research and drug discovery. This protocol is a step-by-step guide on how to use the Web-server predictors in the Cell-PLoc package. The computational time for each prediction is less than 5 s in most cases. The Cell-PLoc package is freely accessible at http://chou.med.harvard.edu/bioinf/Cell-PLoc.
蛋白质亚细胞定位信息对分子细胞生物学、蛋白质组学、系统生物学及药物研发都很重要。为在这些领域为绝大多数实验科学家提供一个用户友好型工具，我们展示了一组最近通过将“高级”方法与从头预测方法相结合而开发的网络服务器程序包。该程序包名为Cell-PLoc，包含以下六个预测器：Euk-mPLoc、Hum-mPLoc、Plant-PLoc、Gpos-PLoc、Gneg-PLoc和Virus-PLoc，分别专门用于真核生物、人类、植物、革兰氏阳性菌、革兰氏阴性菌和病毒蛋白。使用这些网络服务器，人们可以轻松获得预期准确率较高的所需预测结果，这在一系列对基准数据集的交叉验证测试中得到了证明，这些基准数据集涵盖多达22个亚细胞定位位点，且同一亚细胞定位子集中包含的蛋白质之间的序列同一性均不超过或等于25%。其中一些网络服务器还可特别用于处理多重定位蛋白，这些蛋白可能同时存在于两个或更多不同亚细胞位置，或在这些位置之间移动。具有多个定位或此类动态特征的蛋白质特别有趣，因为它们可能具有一些特殊生物学功能，这对基础研究和药物研发领域的研究人员来说都很有吸引力。本方案是关于如何使用Cell-PLoc程序包中的网络服务器预测器的分步指南。大多数情况下，每次预测的计算时间少于5秒。可通过http://chou.med.harvard.edu/bioinf/Cell-PLoc免费访问Cell-PLoc程序包。
