Kernel-based machine learning protocol for predicting DNA-binding proteins

Nucleic Acids Research

Volumn 33, Issue 20, 2005, Pages 6486-6493

  Bhardwaj, Nitin ^a   Langlois, Robert E ^a   Zhao, Guijun ^a   Lu, Hui ^a  

^a University of Illinois at Chicago   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN;

ARTICLE; CELL ACTIVITY; DNA BINDING; DNA REPLICATION; DNA VECTOR; GENE CONTROL; GENE EXPRESSION; MACHINE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; VALIDATION PROCESS;

AMINO ACIDS; ARTIFICIAL INTELLIGENCE; COMPUTATIONAL BIOLOGY; DNA-BINDING PROTEINS; ELECTROSTATICS; MODELS, MOLECULAR; REPRODUCIBILITY OF RESULTS;

EID: 29144504328     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki949     Document Type: Article

References (41)

1. Luscombel,N.M., Austin,S.E., Berman,H.M. and Thornton,J.M. (2000) An overview of the structures of protein-DNA complexes. Genome Biol., 1, 1-37.
2. Jones,S., Heyningen,P., Berman,H.M. and Thornton,J.M. (1999) Protein-DNA interactions: a structural analysis. J. Mol. Biol., 287, 877-896.
3. Siggers,T.W., Silkov,A. and Honig,B. (2005) Structural alignment of protein-DNA interfaces: insights into the determinants of binding specificity. J. Mol. Biol., 345, 1027-1045.
4. Pabo,C.O. and Nekludova,L. (2000) Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? J. Mol. Biol, 301, 597-624.
5. Nadassy,K, Wodak,S.J. and Janin,J. (1999) Structural features of protein-nucleic acid recognition sites. Biochemistry, 38, 1999-2017.
6. Alexander,M.K., Bourns,B.D. and Zakian,V.A. (2001) One-hybrid systems for detecting protein-DNA interactions. Methods Mol. Biol., 177, 241-259.
7. Sathyapriya,R. and Vishveshwara,S. (2004) Interaction of DNA with clusters of amino acids in proteins. Nucleic Acids Res., 32, 4109-4118.
8. Havranek,J.J., Duarte,C.M. and Baker,D.J. (2004) A simple physical model for the prediction and design of protein-DNA interactions. J. Mol Biol., 344, 59-70.
9. Benos,P.V., Lapedes,A.S. and Stormo,G.D. (2002) Is there a code for protein-DNA recognition? Probab(ilistical)ly Bioessays, 24, 466-475.
10. Paillard,G. and Lavery,R. (2004) Analyzing protein-DNA recognition mechanisms. Structure, 12, 113-22.
11. Djordjevic,M., Sengupta,A.M. and Shraiman,B.I. (2003) A biophysical approach to transcription factor binding site discovery. Genome Res., 13, 2381-2390.
12. Marcotte,E.M., Pellegrini,M., Ng,H.-L., Rice,D.W., Yeates,T.O. and Eisenberg,D. (1999) Detecting protein function and protein-protein interactions from genome sequences. Science, 285, 751-753.
13. Lu,X., Zhai,C., Gopalakrishnan,V. and Buchanan,B.G. (2004) Automatic annotation of protein motif function with Gene Ontology terms. BMC Bioinformatics, 5, 122.
14. Pellegrini,M., Marcotte,E.M., Thompson,M.J., Eisenberg,D. and Yeates,T.O. (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl Acad. Sci. USA, 96, 4285-4288.
15. Cai,Y. and Lin,S.L. (2003) Support vector machines for predicting rRNA-, RNA-, and DNA-binding proteins from amino acid sequences. Biochim. Biophys. Acta., 1648, 127-133.
16. Ahmad,S., Gromiha,M.M. and Sarai,A. (2004) Analysis of DNA-binding proteins and their binding residues based on composition, sequence and structural information. Bioinformatics, 20, 477-486.
17. Stawiski,E.W., Gregoret,L.M. and Mandel-Gutfreund,Y. (2003) Annotating nucleic acid-binding function based on protein structure. J. Mol. Bio., 326, 1065-1079.
18. Jones,S., Shanahan,H.P., Berman,H.M. and Thornton,J.M. (2003) Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. Nucleic Acids Res., 31, 7189-7198.
19. Ahmad,S. and Sarai,A. (2004) Moment-based prediction of DNA-binding proteins. J. Mol. Biol., 341, 65-71.
20. Tsuchiya,Y., Kinoshita,K. and Nakamura,H. (2004) Structure-based prediction of DNA-binding sites on proteins using empirical preference of electrostatic potential and the shape of molecular surfaces. Proteins, 55, 885-894.
21. Vapnik,V. and Cortes,C. (1995) Support vector networks. Machine Learning, 20, 273-293.
22. Dubchak,I., Muchnik,I., Mayor,C., Dralyuk,J. and Kim,S.-H. (1999) Recognition of a protein fold in the context of the Structural Classification of Proteins (SCOP) classification. Proteins, 35, 401-407.
23. Brown,M.P., Grundy,W.N., Lin,D., Cristianini,N., Sugnet,C.W., Furey,T.S., Ares,M.Jr and Haussler,D. (2000) Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc. Natl Acad. Sci. USA, 97, 262-267.
24. Jaakkola,T., Diekhans,M. and Haussler,D. (1999) Using the Fisher kernel method to detect remote protein homologies. Proc. Seventh Int. Conf. Intell. Syst. Mol. Biol., AAAI Press, Menlo Park, CA, 149-158.
25. Ding,C.H.Q. and Dubchak,I. (2001) Multi-class protein fold recognition using support vector machines and neural networks. Bioinformatics, 17, 349-358.
26. Langlois,R.E., Diec,A., Perisic,O., Dai,Y. and Lu,H. (2005) Improved Protein Fold Assignment Using Support Vector Machines. Int J Bioinformatics Research and Applications, (In Press).
27. Jones,S., Shanahan,H.P., Berman,H.M. and Thornton,J.M. (2003) Using electrostatic potentials to predict DNA-binding site on DNA-binding proteins. Nucleic Acids. Res., 31, 7189-7198.
28. Word,J.M., Lovell,S.C., Richardson,J.S. and Richardson,D.C. (1999) Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J. Mol. Biol, 285, 1735-1747.
29. Brooks,B., Bruccoleri,R.E., Olafson,B., States,D., Swaminathan,S. and Karplus,M. (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem., 4, 187-217.
30. Gilson,M., Sharp,K. and Honig,B. (1988) Calculating electrostatic interactions in bio-molecules: method and error assessment. J. Comput. Chem., 9, 327-335.
31. Jayaram,B., Sharp,K.A. and Honig,B. (1989) The electrostatic potential of B-DNA. Biopolymers, 28, 975-993.
32. Sharp,K.A. and Honig,B. (1990) Electrostatic interactions in macromolecules: theory and applications. Annu. Rev. Biophys. Biophys. Chem., 19, 301-332.
33. Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
34. Cristianini,N. and Shawe-Taylor,J. (1999) An Introduction to Support Vector Machines and Other Kernel-Based Learning Methods. Cambridge University Press, Cambridge, UK.
35. Chang,C.-C. and Lin,C.-J. (2005) LIBSVM: A Library for Support Vector Machines. Technical Report. Department of Computer Science, National Taiwan University.
36. Chen,Y., Kortemme,T., Robertson,T., Baker,D. and Varani,G. (2004) 'A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys'. Nucleic. Acids Res., 32, 5145-6162.
37. Maiti,R., Van Domselaar,G.H., Zhang,H. and Wishart,D.S. (2004) SuperPose: a simple server for sophisticated structural superposition. Nucleic Acids Res., 32, W590-594.
38. Bhardwaj,N., Langlois,R.E., Zhao,G. and Lu,H. (2005) Structure Based Prediction of Binding Residues on DNA-binding Proteins. 27th Annual International Conference of the Engineering in Medicine and Biology Society, (in press).
39. Harrison,S.C. (1991) A structural taxonomy of DNA-binding domains. Nature, 353, 715-719.
40. Jones,S., Barker,J.A., Nobeli,I. and Thornton,J.M. (2003) Using structural motif templates to identify proteins with DNA binding function. Nucleic Acids Res., 31, 2811-2823.
41. Humphrey,W., Dalke,A. and Schulten,K. (1996) VMD: visual molecular dynamics. J. Mol. Graph., 14, 33-38.