Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms.
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.
Chou
Kuo-Chen
KC
Gordon Life Science Institute, 13784 Torrey Del Mar Drive, San Diego, California 92130, USA. kcchou@gordonlifescience.org
Shen
Hong-Bin
HB
D000818:Animals; D001419:Bacteria; D002477:Cells / Q000737:chemistry; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D010363:Pattern Recognition, Automated / Q000379:methods*; D010944:Plants; D011506:Proteins / Q000032:analysis* / Q000235:genetics; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D013329:Structure-Activity Relationship; D013347:Subcellular Fractions / Q000737:chemistry; D014780:Viruses
D011506:Proteins