User:Lonsbio/sandbox
Software
[edit]| Name | Year | Description | Target | References |
|---|---|---|---|---|
| APSLAP | Prediction of apoptosis protein sub cellular Localization | [1] | ||
| Cell-PLoc | A package of web-servers for predicting subcellular localization of proteins in various organisms. | [2] | ||
| BaCelLo | Prediction of eukaryotic protein subcellular localization. Unlike other methods, the predictions are balanced among different classes and all the localizations that are predicted are considered as equiprobable, to avoid mispredictions. | [3] | ||
| CELLO | CELLO uses a two-level Support Vector Machine system to assign localizations to both prokaryotic and eukaryotic proteins. | [4] [5] | ||
| ClubSub-P | ClubSub-P is a database of cluster-based subcellular localization (SCL) predictions for Archaea and Gram negative bacteria. | [6] | ||
| Euk-mPLoc 2.0 | Predicting the subcellular localization of eukaryotic proteins with both single and multiple sites. | [7] | ||
| CoBaltDB | CoBaltDB is a novel powerful platform that provides easy access to the results of multiple localization tools and support for predicting prokaryotic protein localizations. | [8] | ||
| HSLpred | This method allow to predict subcellular localization of human proteins. This method combines power of composition based SVM models and similarity search techniques PSI-BLAST. | [9] | ||
| KnowPredsite | A knowledge-based approach to predict the localization site(s) of both single-localized and multi-localized proteins for all eukaryotes. | [10] | ||
| LOCtree | Prediction based on mimicking the cellular sorting mechanism using a hierarchical implementation of support vector machines. LOCtree is a comprehensive predictor incorporating predictions based on PROSITE/PFAM signatures as well as SwissProt keywords. | [11] | ||
| LocTree2/3 | Subcellular localization prediction for all proteins in all domains of life. LocTree2/3 predicts 3 classes for Archaea, 6 for Bacteria and 18 for Eukaryota | [12] [13] | ||
| MultiLoc | An SVM-based prediction engine for a wide range of subcellular locations. | [14] | ||
| PSORT | The first widely used method for protein subcellular localization prediction, developed under the leadership of Kenta Nakai. Now researchers are also encouraged to use other PSORT programs such as WoLF PSORT and PSORTb for making predictions for certain types of organisms (see below). PSORT prediction performances are lower than those of recently developed predictors. | [15] | ||
| PSORTb | Prediction of bacterial protein localization. | [16] [17] | ||
| MetaLocGramN | Meta subcellular localization predictor of Gram-negative protein. MetaLocGramN is a gateway to a number of primary prediction methods (various types: signal peptide, beta-barrel, transmembrane helices and subcellular localization predictors). In author's benchmark, MetaLocGramN performed better in comparison to other SCL predictive methods, since the average Matthews correlation coefficient reached 0.806 that enhanced the predictive capability by 12% (compared to PSORTb3). MetaLocGramN can be run via SOAP. | [18] | ||
| PredictNLS | Prediction of nuclear localization signals. | [19] | ||
| Proteome Analyst | Prediction of protein localization for both prokaryotes and eukaryotes using a text mining approach. | [20] | ||
| SCLPred | SCLpred protein subcellular localization prediction by N-to-1 neural networks. | [21] | ||
| SecretomeP | Prediction of eukaryotic proteins that are secreted via a non-traditional secretory mechanism. | [22] | ||
| SherLoc | An SVM-based predictor combining MultiLoc with text-based features derived from PubMed abstracts. | [23] | ||
| SCLAP | An Adaptive Boosting Method for Predicting Subchloroplast Localization of Plant Proteins. | [24] | ||
| TargetP | Prediction of N-terminal sorting signals. | [25] | ||
| TMHMM | Prediction of transmembrane helices to identify transmembrane proteins. | |||
| WoLF PSORT | An updated version of PSORT/PSORT II for the prediction of eukaryotic sequences. | [26] |
Application
[edit]Determining subcellular localization is important for understanding protein function and is a critical step in genome annotation.
Knowledge of the subcellular localization of a protein can significantly improve target identification during the drug discovery process. For example, secreted proteins and plasma membrane proteins are easily accessible by drug molecules due to their localization in the extracellular space or on the cell surface.
Bacterial cell surface and secreted proteins are also of interest for their potential as vaccine candidates or as diagnostic targets.
Aberrant subcellular localization of proteins has been observed in the cells of several diseases, such as cancer and Alzheimer's disease.
Secreted proteins from some archaea that can survive in unusual environments have industrially important applications.
Databases
[edit]Curated protein subcellular locations can be searched in UniProtKB. There are several computationally predicted protein subcellular location databases including the fungal secretome and subcellular proteome knowledgebase (FunSecKB2), the plant secretome and subcellular proteome knowledgebase (PlantSecKB), MetazSecKB for human and animals, and the lactic acid bacterial secretome database. Though there are some inaccuracies in the computational prediction, these databases provide useful resources for further characterizing the protein subcellular locations.
References
[edit]- ^ Saravanan V, Lakshmi PTV (Dec 2013). "APSLAP". Acta Biotheor. 61 (4): 481–97. doi:10.1007/s10441-013-9197-1. PMID 23982307.
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chou1was invoked but never defined (see the help page). - ^ Pierleoni A, Martelli PL, Fariselli P, Casadio R (July 2006). "BaCelLo". Bioinformatics. 22 (14): e408–16. doi:10.1093/bioinformatics/btl222. PMID 16873501.
{{cite journal}}: Cite has empty unknown parameter:|1=(help); Text "a balanced subcellular localization predictor" ignored (help)CS1 maint: multiple names: authors list (link) - ^ Yu CS, Lin CJ, Hwang JK (May 2004). "Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions". Protein Sci. 13 (5): 1402–6. doi:10.1110/ps.03479604. PMC 2286765. PMID 15096640.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Yu CS, Chen YC, Lu CH, Hwang JK (August 2006). "Prediction of protein subcellular localization". Proteins. 64 (3): 643–51. doi:10.1002/prot.21018. PMID 16752418.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Nagarajan Paramasivam, Dirk Linke (2011). "ClubSub-P is a database of cluster-based subcellular localization (SCL) predictions for Archaea and Gram negative bacteria". Frontiers in Microbiology. 2: 218. doi:10.3389/Ffmicb.2011.00218. PMC 3210502. PMID 22073040.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ Chou KC, Shen HB (2010). "A new method for predicting the subcellular localization of eukaryotic proteins with both single and multiple sites". PLoS ONE. 5 (4): e9931. doi:10.1371/journal.pone.0009931. PMC 2848569. PMID 20368981.
{{cite journal}}: Cite has empty unknown parameter:|1=(help); Text "Euk-mPLoc 2.0" ignored (help)CS1 maint: unflagged free DOI (link) - ^ Goudenège D, Avner S, Lucchetti-Miganeh C, Barloy-Hubler F (2010). "CoBaltDB". BMC Microbiol. 10: 88. doi:10.1186/1471-2180-10-88. PMC 2850352. PMID 20331850.
{{cite journal}}: Cite has empty unknown parameter:|1=(help); Text "Complete bacterial and archaeal orfeomes subcellular localization database and associated resources" ignored (help)CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link) - ^ Garg A, Bhasin M, Raghava GP (April 2005). "Support vector machine-based method for subcellular localization of human proteins using amino acid compositions, their order, and similarity search". J. Biol. Chem. 280 (15): 14427–32. doi:10.1074/jbc.M411789200. PMID 15647269.
{{cite journal}}: CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link) - ^ Lin HN, Chen CT, Sung TY, Ho SY, and Hsu WL. (December 2009). [http "Protein subcellular localization prediction of eukaryotes using a knowledge-based approach"]. BMC Bioinformatics. 10: S8. doi:10.1186/1471-2105-10-S15-S8. PMC 2788359. PMID 19958518.
{{cite journal}}: Check|url=value (help); Cite has empty unknown parameter:|1=(help); Text "//www.biomedcentral.com/1471-2105/10/S15/S8" ignored (help)CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link) - ^ Nair R, Rost B (April 2005). "Mimicking cellular sorting improves prediction of subcellular localization". J. Mol. Biol. 348 (1): 85–100. doi:10.1016/j.jmb.2005.02.025. PMID 15808855.
- ^ Goldberg T, Hamp T, Rost B (2012). "LocTree2 predicts localization for all domains of life". Bioinformatics. 28 (18): i458–i465. doi:10.1093/bioinformatics/bts390. PMC 3436817. PMID 22962467.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Goldberg T, Hecht M, Hamp T, Karl T, Yachdav G, Nielsen H, Rost B; et al. (2014). "LocTree3 prediction of localization". Nucleic Acids Research. 42 (Web Server issue): W350–5. doi:10.1093/nar/gku396. PMID 24848019.
{{cite journal}}: Explicit use of et al. in:|author=(help)CS1 maint: multiple names: authors list (link) - ^ Höglund A, Dönnes P, Blum T, Adolph HW, Kohlbacher O (May 2006). "MultiLoc". Bioinformatics. 22 (10): 1158–65. doi:10.1093/bioinformatics/btl002. PMID 16428265.
{{cite journal}}: Cite has empty unknown parameter:|1=(help); Text "prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition" ignored (help)CS1 maint: multiple names: authors list (link) - ^ Nakai K, Kanehisa M (1991). "Expert system for predicting protein localization sites in gram-negative bacteria". Proteins. 11 (2): 95–110. doi:10.1002/prot.340110203. PMID 1946347.
- ^ Gardy JL, Spencer C, Wang K, Ester M, Tusnády GE, Simon I, Hua S, deFays K, Lambert C, Nakai K, Brinkman FS (July 2003). "PSORT-B". Nucleic Acids Res. 31 (13): 3613–7. doi:10.1093/nar/gkg602. PMC 169008. PMID 12824378.
{{cite journal}}: Cite has empty unknown parameter:|1=(help); Text "Improving protein subcellular localization prediction for Gram-negative bacteria" ignored (help)CS1 maint: multiple names: authors list (link) - ^ Gardy JL, Laird MR, Chen F, Rey S, Walsh CJ, Ester M, Brinkman FS (March 2005). "PSORTb v.2.0". Bioinformatics. 21 (5): 617–23. doi:10.1093/bioinformatics/bti057. PMID 15501914.
{{cite journal}}: Cite has empty unknown parameter:|1=(help); Text "expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis" ignored (help)CS1 maint: multiple names: authors list (link) - ^ Magnus M, Pawlowski M, Bujnicki JM (December 2012). [http "MetaLocGramN"]. BBA - Proteins and Proteomics. 1824 (12): 1425–33. doi:10.1016/j.bbapap.2012.05.018. PMID 22705560.
{{cite journal}}: Check|url=value (help); Cite has empty unknown parameters:|1=and|3=(help); Text "//www.sciencedirect.com/science/article/pii/S1570963912001185" ignored (help); Text "a meta-predictor of protein subcellular localization for Gram-negative bacteria" ignored (help)CS1 maint: multiple names: authors list (link) - ^ Nair R, Carter P, Rost B (January 2003). "NLSdb". Nucleic Acids Res. 31 (1): 397–9. doi:10.1093/nar/gkg001. PMC 165448. PMID 12520032.
{{cite journal}}: Cite has empty unknown parameter:|1=(help); Text "database of nuclear localization signals" ignored (help)CS1 maint: multiple names: authors list (link) - ^ Lu Z, Szafron D, Greiner R, Lu P, Wishart DS, Poulin B, Anvik J, Macdonell C, Eisner R (March 2004). "Predicting subcellular localization of proteins using machine-learned classifiers". Bioinformatics. 20 (4): 547–56. doi:10.1093/bioinformatics/btg447. PMID 14990451.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Mooney C, Wang YH, Pollastri G. (October 2011). "SCLpred". Bioinformatics. 27 (20): 2812–9. doi:10.1093/bioinformatics/btr494. PMID 21873639.
{{cite journal}}: Cite has empty unknown parameter:|1=(help); Text "protein subcellular localization prediction by N-to-1 neural networks." ignored (help)CS1 maint: multiple names: authors list (link) - ^ Bendtsen JD, Jensen LJ, Blom N, Von Heijne G, Brunak S (April 2004). "Feature-based prediction of non-classical and leaderless protein secretion". Protein Eng. Des. Sel. 17 (4): 349–56. doi:10.1093/protein/gzh037. PMID 15115854.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Shatkay H, Höglund A, Brady S, Blum T, Dönnes P, Kohlbacher O (June 2007). "SherLoc". Bioinformatics. 23 (11): 1410–7. doi:10.1093/bioinformatics/btm115. PMID 17392328.
{{cite journal}}: Cite has empty unknown parameter:|1=(help); Text "high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data" ignored (help)CS1 maint: multiple names: authors list (link) - ^ Saravanan V, Lakshmi PTV (Jan 2013). "SCLAP". OMICS. 17 (2): 106–15. doi:10.1089/omi.2012.0070. PMID 23289782.
{{cite journal}}: Cite has empty unknown parameter:|1=(help); Text "An Adaptive Boosting Method for Predicting Subchloroplast Localization of Plant Proteins" ignored (help) - ^ Emanuelsson O, Nielsen H, Brunak S, von Heijne G (July 2000). "Predicting subcellular localization of proteins based on their N-terminal amino acid sequence". J. Mol. Biol. 300 (4): 1005–16. doi:10.1006/jmbi.2000.3903. PMID 10891285.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K (July 2007). "WoLF PSORT". Nucleic Acids Res. 35 (Web Server issue): W585–7. doi:10.1093/nar/gkm259. PMC 1933216. PMID 17517783.
{{cite journal}}: Cite has empty unknown parameter:|1=(help); Text "protein localization predictor" ignored (help)CS1 maint: multiple names: authors list (link)
Further reading
[edit]- Bork P, Dandekar T, Diaz-Lazcoz Y, Eisenhaber F, Huynen M, Yuan Y (November 1998). "Predicting function: from genes to genomes and back". J. Mol. Biol. 283 (4): 707–25. doi:10.1006/jmbi.1998.2144. PMID 9790834.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - Nakai K (2000). "Protein sorting signals and prediction of subcellular localization". Adv. Protein Chem. 54: 277–344. doi:10.1016/s0065-3233(00)54009-1. PMID 10829231.
- Emanuelsson O (December 2002). "Predicting protein subcellular localisation from amino acid sequence information". Brief. Bioinformatics. 3 (4): 361–76. doi:10.1093/bib/3.4.361. PMID 12511065.
- Schneider G, Fechner U (June 2004). "Advances in the prediction of protein targeting signals". Proteomics. 4 (6): 1571–80. doi:10.1002/pmic.200300786. PMID 15174127.
- Gardy JL, Brinkman FS (October 2006). "Methods for predicting bacterial protein subcellular localization". Nat. Rev. Microbiol. 4 (10): 741–51. doi:10.1038/nrmicro1494. PMID 16964270.
- Chou KC, Shen HB (November 2007). "Recent progress in protein subcellular location prediction". Anal. Biochem. 370 (1): 1–16. doi:10.1016/j.ab.2007.07.006. PMID 17698024.
Category:Protein methods Category:Cell biology Category:Bioinformatics Category:Computational science Category:Bioinformatics software Category:Protein targeting