title: SubMito-PSPCP: predicting protein submitochondrial locations by hybridizing positional specific physicochemical properties with pseudoamino acid compositions.
abstract: Knowing the submitochondrial location of a mitochondrial protein is an important step in understanding its function. We developed a new method for predicting protein submitochondrial locations by introducing a new concept: positional specific physicochemical properties. With the framework of general form pseudoamino acid compositions, our method used only about 100 features to represent protein sequences, which is much simpler than the existing methods. On the dataset of SubMito, our method achieved over 93% overall accuracy, with 98.60% for inner membrane, 93.90% for matrix, and 70.70% for outer membrane, which are comparable to all state-of-the-art methods. As our method can be used as a general method to upgrade all pseudoamino-acid-composition-based methods, it should be very useful in future studies. We implement our method as an online service: SubMito-PSPCP.
authors.affiliation: School of Computer Science and Technology, Tianjin University, Tianjin 300072, China ; Tianjin Key Laboratory of Cognitive Computing and Application, Tianjin University, Tianjin 300072, China.
authors.forename: Pufeng
authors.initials: P
authors.lastname: Du
authors.forename: Yuan
authors.initials: Y
authors.lastname: Yu
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology; D030562:Databases, Protein; D024101:Mitochondrial Proteins / Q000648:ultrastructure*; D020539:Sequence Analysis, Protein
chemical_list: D024101:Mitochondrial Proteins
references.citation: J Theor Biol. 2009 Jul 21;259(2):366-72
references.pmid: 19341746
references.citation: Mol Biosyst. 2013 Apr 5;9(4):634-44
references.pmid: 23370050
references.citation: Protein Eng Des Sel. 2007 Nov;20(11):561-7
references.pmid: 17993650
references.citation: Mol Biosyst. 2012 Feb;8(2):629-41
references.pmid: 22134333
references.citation: Amino Acids. 2008 May;34(4):653-60
references.pmid: 18175047
references.citation: Mol Biosyst. 2011 Dec;7(12):3287-97
references.pmid: 21984117
references.citation: Nature. 2003 Nov 13;426(6963):127-8
references.pmid: 14614484
references.citation: Expert Rev Proteomics. 2013 Jun;10(3):227-37
references.pmid: 23777214
references.citation: Proteomics. 2008 Apr;8(8):1564-75
references.pmid: 18348319
references.citation: J Theor Biol. 2012 Nov 21;313:61-7
references.pmid: 22960368
references.citation: Proteins. 2001 May 15;43(3):246-55
references.pmid: 11288174
references.citation: Nucleic Acids Res. 2013 Apr 1;41(6):e68
references.pmid: 23303794
references.citation: J Theor Biol. 2011 Mar 21;273(1):236-47
references.pmid: 21168420
references.citation: PLoS One. 2012;7(5):e36317
references.pmid: 22629314
references.citation: J Theor Biol. 2011 Jan 21;269(1):208-16
references.pmid: 21040732
references.citation: Expert Rev Proteomics. 2011 Jun;8(3):391-404
references.pmid: 21679119
references.citation: Biochim Biophys Acta. 2011 Mar;1813(3):424-30
references.pmid: 21255619
references.citation: Bioinformatics. 2005 Jan 1;21(1):10-9
references.pmid: 15308540
references.citation: Amino Acids. 2012 Aug;43(2):545-55
references.pmid: 22102053
references.citation: Expert Rev Proteomics. 2007 Aug;4(4):453-63
references.pmid: 17705704
references.citation: PLoS One. 2011 Mar 30;6(3):e18258
references.pmid: 21483473
references.citation: J Proteomics. 2012 Dec 21;77:321-8
references.pmid: 23000219
references.citation: PLoS One. 2012;7(1):e31057
references.pmid: 22303481
references.citation: Acta Biotheor. 2013 Jun;61(2):259-68
references.pmid: 23475502
references.citation: IEEE Trans Nanobioscience. 2012 Sep;11(3):237-43
references.pmid: 22987129
references.citation: J Mol Cell Cardiol. 2001 Jun;33(6):1065-89
references.pmid: 11444914
references.citation: Protein Pept Lett. 2013 Mar;20(3):309-17
references.pmid: 22591474
references.citation: J Theor Biol. 2012 Jan 21;293:121-30
references.pmid: 22037046
references.citation: Curr Biol. 2006 Jul 25;16(14):R551-60
references.pmid: 16860735
references.citation: Genome Res. 2013 Aug;23(8):1283-94
references.pmid: 23674306
references.citation: Nat Biotechnol. 2003 Mar;21(3):281-6
references.pmid: 12592411
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Bioinformatics. 2000 May;16(5):412-24
references.pmid: 10871264
references.citation: Bioinformatics. 2011 May 1;27(9):1224-30
references.pmid: 21367869
references.citation: Mol Biosyst. 2013 Jun;9(6):1092-100
references.pmid: 23536215
references.citation: BMC Bioinformatics. 2006 Nov 30;7:518
references.pmid: 17134515