Identification of efflux proteins using efficient radial basis function networks with position-specific scoring matrices and biochemical properties

Proteins: Structure, Function and Bioinformatics

Volumn 81, Issue 9, 2013, Pages 1634-1643

  Ou, Yu Yen ^a   Chen, Shu An ^a   Chang, Yun Min ^a   Velmurugan, Devadasan ^b   Fukui, Kazuhiko ^c   Michael Gromiha, M ^d  

^a YUAN ZE UNIVERSITY   (Taiwan)

^b UNIVERSITY OF MADRAS   (India)

^c NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^d INDIAN INSTITUTE OF TECHNOLOGY MADRAS   (India)

Author keywords

Annotation; E. coli; Genome; Membrane protein; Transporter

Indexed keywords

AMINO ACID; CARRIER PROTEIN; EFFLUX PROTEIN; MEMBRANE PROTEIN; UNCLASSIFIED DRUG;

AMINO ACID COMPOSITION; ARTICLE; BACTERIAL GENOME; BIOCHEMICAL COMPOSITION; COMPARATIVE STUDY; ESCHERICHIA COLI; NONHUMAN; POSITION WEIGHT MATRIX; PRIORITY JOURNAL; PROTEIN ANALYSIS; PSEUDOMONAS AERUGINOSA;

ANNOTATION; E. COLI; GENOME; MEMBRANE PROTEIN; TRANSPORTER;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MEMBRANE TRANSPORT PROTEINS; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; POSITION-SPECIFIC SCORING MATRICES; SEQUENCE ANALYSIS, PROTEIN;

EID: 84882822778     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24322     Document Type: Article

References (40)

1. Bhardwaj AK, Mohanty P. Bacterial efflux pumps involved in multidrug resistance and their inhibitors: rejuvinating the antimicrobial chemotherapy. Recent Pat Antiinfect Drug Discov 2012;7:73-89.
2. Gromiha MM, Yabuki Y, Suresh MX, Thangakani AM, Suwa M, Fukui K. TMFunction: database for functional residues in membrane proteins. Nucl Acids Res 2009;37:D201-D204.
3. Koike K, Conseil GL, Leslie EM, Deeley RG, Cole SPC. Identification of proline residues in the core cytoplasmic and transmembrane regions of multidrug resistance protein 1 (MRP1/ABCC1) important for transport function, substrate specificity, and nucleotide interactions. J Biol Chem 2004;279:12325-12336.
4. Zhang DW, Gu HM, Situ D, Haimeur A, Cole SPC, Deeley RG. Functional importance of polar and charged amino acid residues in transmembrane helix 14 of multidrug resistance protein 1 (MRP1/ABCC1) - Identification of an aspartate residue critical for conversion from a high to low affinity substrate binding state. J Biol Chem 2003;278:46052-46063.
5. Yang YY, Chen Q, Zhang JT. Structural and functional consequences of mutating cysteine residues in the amino terminus of human multidrug resistance-associated protein 1. J Biol Chem 2002;277:44268-44277.
6. Yang RY, Scavetta R, Chang XB. Interaction between the bound Mg center dot ATP and the Walker A serine residue in NBD2 of multidrug resistance-associated protein MRP1 plays a crucial role for the ATP-dependent leukotriene C4 transport. Biochemistry 2008;47:8456-8464.
7. Sharom FJ. The P-glycoprotein multidrug transporter. Essays Biochem 2011;50:161-178.
8. Bador J, Amoureux L, Duez JM, Drabowicz A, Siebor E, Llanes C, Neuwirth C. First description of an RND-type multidrug efflux pump in achromobacter xylosoxidans, AxyABM. Antimicro Agents Chemother 2011;55:4912-4914.
9. Murakami S, Nakashima R, Yamashita E, Yamaguchi A. Crystal structure of bacterial multidrug efflux transporter AcrB. Nature 2002;419:587-593.
10. Murakami S, Nakashima R, Yamashita E, Matsumoto T, Yamaguchi A. Crystal structures of a multidrug transporter reveal a functionally rotating mechanism. Nature 2006;443:173-179.
11. Bikadi Z, Hazai I, Malik D, Jemnitz K, Veres Z, Hari P, Ni ZL, Loo TW, Clarke DM, Hazai E, Mao QC. Predicting P-glycoprotein-mediated drug transport based on support vector machine and three-dimensional crystal structure of P-glycoprotein. PLoS One 2011;6:e25815.
12. Baker J, Wright SH, Tama F. Simulations of substrate transport in the multidrug transporter EmrD. Proteins 2012;80, 1620-1632.
13. Li HQ, Benedito VA, Udvardi MK, Zhao PX. TransportTP: a two-phase classification approach for membrane transporter prediction and characterization. BMC Bioinf 2009;10:418.
14. Gromiha MM, Yabuki Y. Functional discrimination of membrane proteins using machine learning techniques. BMC Bioinf. 2008;9:135.
15. Ou YY, Chen SA, Gromiha MM. Classification of transporters using efficient radial basis function networks with position-specific scoring matrices and biochemical properties. Proteins 2010;78:1789-1797.
16. Li HQ, Dai XB, Zhao XC. A nearest neighbor approach for automated transporter prediction and categorization from protein sequences. Bioinformatics 2008;24:1129-1136.
17. Chen SA, Ou YY, Lee TY, Gromiha MM. Prediction of transporter targets using efficient RBF networks with PSSM profiles and biochemical properties. Bioinformatics 2011;27:2062-2067.
18. Consortium U. Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res 2011;39:D214-D219.
19. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-3402.
20. Ou Y-Y. QuickRBF: a package for efficient radial basis function networks. QuickRBF software. Available at: http://csieorg/yien/quickrbf/, 2005. Accessed on 10 April 2013.
21. Ou Y-Y. A novel radial basis function network classifier with centers set by hierarchical clustering. Proc IEEE Int Conf Neural Netw 2005;3:1383-1388.
22. Yang ZR, Thomson R. Bio-basis function neural network for prediction of protease cleavage sites in proteins. IEEE Trans Neural Netw 2005;16:263-274.
23. Zhang GZ, Huang DS. Prediction of inter-residue contacts map based on genetic algorithm optimized radial basis function neural network and binary input encoding scheme. J Comput Aided Mol Des 2004;18:797-810.
24. Su CT, Chen CY, Ou YY. Protein disorder prediction by condensed PSSM considering propensity for order or disorder. BMC Bioinformatics 2006;7:319.
25. Ou YY, Gromiha MM, Chen SA, Suwa M. TMBETADISC-RBF: discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles. Comput Biol Chem 2008;32:227-231.
26. Lee TY, Chen SA, Hung HY, Ou YY. Incorporating distant sequence features and radial basis function networks to identify ubiquitin conjugation sites. PLoS One 2011;6:e17331.
27. Yin J-B, Li T, Shen H-B. Gaussian kernel optimization: complex problem and a simple solution. Neurocomputing 2011;74;3816-3822.
28. Lei, J-B, Yin J-B, Shen H-B. GFO: a data driven approach for optimizing the Gaussian function based similarity metric in computational biology. Neurocomputing 2013;99;307-315.
29. Gromiha MM, Suwa M. A simple statistical method for discriminating outer membrane proteins with better accuracy. Bioinformatics 2005;21:961-968.
30. Gromiha MM. Protein bioinformatics: from sequence to function. New Delhi: Academic Press; 2010.
31. Kumar M, Gromiha MM, Raghava GP. Identification of DNA-binding proteins using support vector machines and evolutionary profiles. BMC Bioinformatics 2007;8:463.
32. Gromiha MM, Ahmad S, Suwa M. Application of residue distribution along the sequence for discriminating outer membrane proteins. Comput Biol Chem 2005;29:135-142.
33. Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202.
34. Xie D, Li A, Wang MH, Fan ZW, Feng HQ. LOCSVMPSI: a web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST. Nucl Acids Res 2005;33:W105-W110.
35. Ou YY, Chen SA, Gromiha MM. Classification of transporters using efficient radial basis function networks with position-specific scoring matrices and biochemical properties. Proteins 2010;78:1789-1797.
36. Kawashima S, Pokarowski P, Pokarowska M, Kolinski A, Katayama T, Kanehisa M. AAindex: amino acid index database, progress report 2008. Nucl Acids Res 2008;36:D202-D205.
37. Lin C-J, Chen Y-W. Combining SVMs with various feature selection strategies. NIPS 2003 Feature Selection Challenge 2003;Vancouver:1-10.
38. He, H, Garcia EA. Learning from Imbalanced Data. IEEE Trans Knowl Data Eng 2009;21:1263-1284.
39. Yu DJ, Hu J, Huang Y, Shen HB, Qi Y, Tang ZM, Yang JY. TargetATPsite: a template-free method for ATP-binding sites prediction with residue evolution image sparse representation and classifier ensemble. J Comput Chem 2013;34:974-985.
40. Witten IH, Frank E. Data mining: practical machine learning tools and techniques. 2nd ed. San Francisco: Morgan Kaufmann; 2005.