Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization.

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 o...

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Autores principales:	Kuo-Chen Chou, Hong-Bin Shen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e5977fcf117e472d96c9c6f54bfabd47
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spelling	oai:doaj.org-article:e5977fcf117e472d96c9c6f54bfabd472021-12-02T20:20:28ZPlant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization.1932-620310.1371/journal.pone.0011335https://doaj.org/article/e5977fcf117e472d96c9c6f54bfabd472010-06-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20596258/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203One 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 sits. 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.Kuo-Chen ChouHong-Bin ShenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 6, p e11335 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Kuo-Chen Chou Hong-Bin Shen Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization.
description	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 sits. 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.
format	article
author	Kuo-Chen Chou Hong-Bin Shen
author_facet	Kuo-Chen Chou Hong-Bin Shen
author_sort	Kuo-Chen Chou
title	Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization.
title_short	Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization.
title_full	Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization.
title_fullStr	Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization.
title_full_unstemmed	Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization.
title_sort	plant-mploc: a top-down strategy to augment the power for predicting plant protein subcellular localization.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/e5977fcf117e472d96c9c6f54bfabd47
work_keys_str_mv	AT kuochenchou plantmplocatopdownstrategytoaugmentthepowerforpredictingplantproteinsubcellularlocalization AT hongbinshen plantmplocatopdownstrategytoaugmentthepowerforpredictingplantproteinsubcellularlocalization
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Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization.

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