Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms
Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms
复制标题
DOI：
10.1038/nprot.2007.494
复制
发表时间：
2008-01-01
期刊：
影响因子：
14.8
通讯作者：
Shen, Hong-Bin
中科院分区：
文献类型：
--
作者：
Chou, Kuo-Chen;Shen, Hong-Bin
蛋白质亚细胞定位信息对分子细胞生物学、蛋白质组学、系统生物学和药物研发都很重要。为了给这些领域的绝大多数实验科学家提供一个用户友好的工具，我们介绍了最近通过将“高级”方法与从头算方法相结合而开发的一套网络服务器。这个软件包名为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、革兰氏阳性细菌、革兰氏阴性细菌和病毒的蛋白质。使用这些网络服务器，人们可以轻松地获得具有较高预期准确性的所需预测结果，正如在基准数据集上进行的一系列交叉验证测试所证明的那样，这些数据集涵盖了多达22个亚细胞定位位点，并且其中所包含的任何蛋白质与同一亚细胞定位子集中的任何其他蛋白质的序列同一性均小于25%。其中一些网络服务器也可特别用于处理多重定位蛋白质，这些蛋白质可能同时存在于两个或多个不同的亚细胞位置，或者在这些位置之间移动。具有多种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的生物学功能，这对基础研究和药物研发的研究人员都很有吸引力。本方案是关于如何使用Cell - PLoc软件包中的网络服务器预测器的逐步指南。在大多数情况下，每次预测的计算时间不到5秒。Cell - PLoc软件包可在http://chou.med.harvard.edu/bioinf/Cell - PLoc免费访问。
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 >= 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.