Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization.
Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization.
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Plant-mPLoc：增强植物蛋白亚细胞定位预测能力的自上而下策略
DOI：
10.1371/journal.pone.0011335
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发表时间：
2010-06-28
期刊：
影响因子：
3.7
通讯作者：
Shen HB
中科院分区：
文献类型：
--
作者：
Chou KC;Shen HB
蛋白质组学和细胞生物学的基本目标之一是确定蛋白质在各种细胞器和途径中的功能。蛋白质的亚细胞位置信息可以为揭示蛋白质的功能和理解它们在细胞网络系统中如何相互作用提供有用的见解。现有的预测植物蛋白亚细胞定位的方法大多只能覆盖3个或4个定位位点，对于同时存在于两个或两个以上不同定位位点的复合蛋白，没有一种方法能够有效地预测。事实上，这种复合蛋白可能具有特殊的生物学功能，值得特别注意。本研究从上述两个方面对现有的植物蛋白亚细胞定位预测方法进行了改进。一个新的预测器称为“植物mPLoc”的开发集成的基因本体信息，功能域信息，和序列进化信息，通过三种不同的模式的伪氨基酸组成。它可用于鉴定植物蛋白质在以下12个定位位点中的位置：（1）细胞膜，（2）细胞壁，（3）叶绿体，（4）细胞质，（5）内质网，（6）细胞外，（7）高尔基体，（8）细胞核，（9）细胞核，（10）过氧化物酶体，（11）质体，（12）液泡。与现有的预测植物蛋白亚细胞定位的方法相比，新的预测器更强大和灵活。特别是，它还具有处理多位置蛋白的能力，这是任何现有的专门用于鉴定植物蛋白亚细胞定位的预测器所无法达到的。作为一个用户友好的网络服务器，Plant-mPLoc可在http://www.csbio.sjtu.edu.cn/bioinf/plant-multi/上免费访问。此外，为了方便绝大多数实验科学家，提供了如何使用Web服务器获得所需结果的分步指南。预计本文提出的Plant-mPLoc预测器将成为植物科学以及所有相关领域中非常有用的工具。
One of the fundamental goals in proteomics and cell biology is to identify the functions of proteins in various cellular organelles and pathways. Information of subcellular locations of proteins can provide useful insights for revealing their functions and understanding how they interact with each other in cellular network systems. Most of the existing methods in predicting plant protein subcellular localization can only cover three or four location sites, and none of them can be used to deal with multiplex plant proteins that can simultaneously exist at two, or move between, two or more different location sites. Actually, such multiplex proteins might have special biological functions worthy of particular notice. The present study was devoted to improve the existing plant protein subcellular location predictors from the aforementioned two aspects. A new predictor called “Plant-mPLoc” is developed by integrating the gene ontology information, functional domain information, and sequential evolutionary information through three different modes of pseudo amino acid composition. It can be used to identify plant proteins among the following 12 location sites: (1) cell membrane, (2) cell wall, (3) chloroplast, (4) cytoplasm, (5) endoplasmic reticulum, (6) extracellular, (7) Golgi apparatus, (8) mitochondrion, (9) nucleus, (10) peroxisome, (11) plastid, and (12) vacuole. Compared with the existing methods for predicting plant protein subcellular localization, the new predictor is much more powerful and flexible. Particularly, it also has the capacity to deal with multiple-location proteins, which is beyond the reach of any existing predictors specialized for identifying plant protein subcellular localization. As a user-friendly web-server, Plant-mPLoc is freely accessible at http://www.csbio.sjtu.edu.cn/bioinf/plant-multi/. Moreover, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results. It is anticipated that the Plant-mPLoc predictor as presented in this paper will become a very useful tool in plant science as well as all the relevant areas.
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影响因子：
14.8
作者：
Chou, Kuo-Chen;Shen, Hong-Bin
通讯作者：
Shen, Hong-Bin
DOI：
10.1016/j.bbrc.2007.06.027
发表时间：
2007-08-24
影响因子：
3.1
作者：
Chou, Kuo-Chen;Shen, Hong-Bin
通讯作者：
Shen, Hong-Bin
DOI：
10.1093/protein/12.2.107
发表时间：
1999-02-01
期刊：
PROTEIN ENGINEERING
影响因子：
--
作者：
Chou, KC;Elrod, DW
通讯作者：
Elrod, DW
影响因子：
7
作者：
Camon, E;Magrane, M;Apweiler, R
通讯作者：
Apweiler, R
影响因子：
1.6
作者：
Ding, Hui;Luo, Liaofu;Lin, Hao
通讯作者：
Lin, Hao