+ Resolve Article
+ Follow Us
Follow on FacebookFollow on Facebook
Follow on TwitterFollow on Twitter

+ Translate
+ Subscribe to Site Feed
GeoScience Most Shared ContentMost Shared Content

MetaLocGramN: A meta-predictor of protein subcellular localization for Gram-negative bacteria

, : MetaLocGramN: A meta-predictor of protein subcellular localization for Gram-negative bacteria. Biochimica et Biophysica Acta 1824(12): 1425-1433

Subcellular localization is a key functional characteristic of proteins. It is determined by signals encoded in the protein sequence. The experimental determination of subcellular localization is laborious. Thus, a number of computational methods have been developed to predict the protein location from sequence. However predictions made by different methods often disagree with each other and it is not always clear which algorithm performs best for the given cellular compartment. We benchmarked primary subcellular localization predictors for proteins from Gram-negative bacteria, PSORTb3, PSLpred, CELLO, and SOSUI-GramN, on a common dataset that included 156 proteins. We found that PSORTb3 performs best on the average, but is outperformed by other methods in predictions of extracellular proteins. This motivated us to develop a meta-predictor, which combines the primary methods by using the logistic regression models, to take advantage of their combined strengths, and to eliminate their individual weaknesses. MetaLocGramN runs the primary methods, and based on their output classifies protein sequences into one of five major localizations of the Gram-negative bacterial cell: cytoplasm, plasma membrane, periplasm, outer membrane, and extracellular space. MetaLocGramN achieves the average Matthews correlation coefficient of .86, i.e. 12% better than the best individual primary method. MetaLocGramN is a meta-predictor specialized in predicting subcellular localization for proteins from Gram-negative bacteria. According to our benchmark, it performs better than all other tools run independently. MetaLocGramN is a web and SOAP server available for free use by all academic users at the URL This article is part of a Special Issue entitled: Computational Methods for Protein Interaction and Structural Prediction. Subcellular localization is a key functional characteristic of proteins. We benchmarked subcellular localization predictors for Gram-negative bacteria. We developed a meta-predictor MetaLocGramN. Our method outperforms all the primary subcellular localization predictors. The web/soap server is freely available at


PMID: 22705560

DOI: 10.1016/j.bbapap.2012.05.018

Other references

Nishino, T.; Devuyst, O., 2007: Clinical application of aquaporin research: aquaporin-1 in the peritoneal membrane. Peritoneal dialysis (PD) is an established mode of renal replacement therapy based on the exchange of fluid and solutes between blood and a dialysate that has been instilled in the peritoneal cavity. The dialysis process involves osmosis, as well...

Chervenak, L., 1993: Hotel technology at the start of the new millennium. By the beginning of the new millennium, hotel technology will be entrenched in every phase of hotel management, marketing, and operations. Powerful new microchips will provide dramatic increases in power per dollar invested. High-speed, high-capac...

Yampolsky, L.Y.; Glazko, G.V.; Fry, J.D., 2012: Evolution of gene expression and expression plasticity in long-term experimental populations of Drosophila melanogaster maintained under constant and variable ethanol stress. Gene expression responds to the environment and can also evolve rapidly in response to altered selection regimes. Little is known, however, about the extent to which evolutionary adaptation to a particular type of stress involves changes in the wi...

Penneau, M.; Pichon, C.; Saint-Andre, J.P.; Simard, C., 1980: "Pseudo-carcinomatous hyperplasia" of the epithelial rests of Malassez. A case of mandibular osteitis is reported, showing histologically, an important pseudo peitheliomatous hyperplasia. A possible histological explanation of this observation is that the inflammatory process may be responsible for an odontogenic cell...

Bangs, O., 1910: New or rare birds from western Columbia. Proceedings of the Biological Society of Washington, 23 71-76

Fatton, B.; Savary, D.; Velemir, L.; Amblard, J.; Accoceberry, M.; Jacquetin, B., 2009: Sexual outcome after pelvic reconstructive surgery. Sexual well-being is an important parameter of women's health and quality of live. Sexual disorders may occur in women with pelvic organ prolapse and/or stress urinary incontinence and also after pelvic reconstructive surgery. Sexual dysfunct...

Kacir; Zahed, 1996: Nucleons at finite temperature. Physical Review. D, Particles and Fields 54(9): 5536-5544

White P.S.; Pickett S.T.A., 1985: Natural disturbance and patch dynamics an introduction. Pickett, S T A And P S White (Ed ) The Ecology Of Natural Disturbance And Patch Dynamics Xv+472p Academic Press, Inc , Publishers: Orlando, Fla , Usa; London, England Illus Maps 3-14

Andrade, C.; Sharma, E., 2016: Serotonin Reuptake Inhibitors and Risk of Abnormal Bleeding. Serotonin reuptake inhibitors (SRIs) increase the risk of abnormal bleeding by lowering platelet serotonin and hence the efficiency of platelet-driven hemostasis; by increasing gastric acidity and possibly gastric ulceration; and by other mechanis...

Frey, H.A.; Tuuli, M.G.; England, S.K.; Roehl, K.A.; Odibo, A.O.; Macones, G.A.; Cahill, A.G., 2016: Factors associated with higher oxytocin requirements in labor. To identify clinical characteristics associated with high maximum oxytocin doses in women who achieve complete cervical dilation. A retrospective nested case-control study was performed within a cohort of all term women at a single center between...