Gneg-mPLoc: A top-down strategy to enhance the quality of predicting subcellular localization of Gram-negative bacterial proteins

作者：Shen, Hong Bin^*; Chou, Kuo Chen

来源：Journal of Theoretical Biology, 2010, 264(2): 326-333.

DOI：10.1016/j.jtbi.2010.01.018

• Multiplex protein
• Homology search
• Representative proteins
• Gene ontology
• Functional domain
• Sequential evolution
• Ensemble classifier
• Fusion approach

By incorporating the information of gene ontology, functional domain, and sequential evolution, a new predictor called Gneg-mPLoc was developed. It can be used to identify Gram-negative bacterial proteins among the following eight locations: (1) cytoplasm, (2) extracellular, (3) fimbrium, (4) flagellum, (5) inner membrane, (6) nucleoid, (7) outer membrane, and (8) periplasm. It can also be used to deal with the case when a query protein may simultaneously exist in more than one location. Compared with the original predictor called Gneg-PLoc, the new predictor is much more powerful and flexible. For a newly constructed stringent benchmark dataset in which none of proteins included has >= 25% pairwise sequence identity to any other in a same subset (location), the overall jackknife success rate achieved by Gneg-mPLoc was 85.5%, which was more than 14% higher than the corresponding rate by the Gneg-PLoc. As a user friendly web-server, Gneg-mPLoc is freely accessible at http://www.csbio.sjtu.edu.cn/bioinf/Gneg-multi/.

• 出版日期2010-5-21
• 单位上海交通大学