Sequence-based prediction of DNA-binding residues in proteins with conservation and correlation information

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 9, Issue 6, 2012, Pages 1766-1775

  Ma, Xin ^a   Guo, Jing ^a   Liu, Hong De ^a   Xie, Jian Ming ^a   Sun, Xiao ^a  

^a SOUTHEAST UNIVERSITY   (China)

Author keywords

DNA binding residues; Evolutionary information; Physicochemical property; Random forest

Indexed keywords

CORRELATION COEFFICIENT; DNA-BINDING; DNA-PROTEIN INTERACTION; EVOLUTIONARY INFORMATION; HYDROPHOBIC PROPERTIES; PHYSICOCHEMICAL PROPERTY; PREDICTION PERFORMANCE; RANDOM FORESTS;

AMINO ACIDS; DECISION TREES; DNA; FORECASTING; GENE EXPRESSION;

PROTEINS;

AMINO ACID; DNA; DNA BINDING PROTEIN;

ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; INTERNET; METABOLISM; METHODOLOGY; PROTEIN BINDING; PROTEIN DATABASE; RECEIVER OPERATING CHARACTERISTIC; SEQUENCE ANALYSIS; STATISTICAL MODEL; SUPPORT VECTOR MACHINE;

AMINO ACIDS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; DNA; DNA-BINDING PROTEINS; HUMANS; INTERNET; MODELS, MOLECULAR; MODELS, STATISTICAL; PROTEIN BINDING; ROC CURVE; SEQUENCE ANALYSIS, PROTEIN; SUPPORT VECTOR MACHINES;

MLCS; MLOWN;

EID: 84880480444     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2012.106     Document Type: Article

References (49)

1. J. Wang and Morigen, "BayesPI-A New Model to Study Protein-DNA Interactions: A Case Study of Condition-Specific Protein Binding Parameters for Yeast Transcription Factors," BMC Bioinformatics, vol. 10, article 345, 2009.
2. L. Zamdborg and P. Ma, "Discovery of Protein-DNA Interactions by Penalized Multivariate Regression," Nucleic Acids Research, vol. 37, no. 16, pp. 5246-5254, Sept. 2009.
3. J.B. Kinney, G. Tkacik, and C.G. Callan Jr., "Precise Physical Models of Protein-DNA Interaction from High-Throughput Data," Proc Nat'l Academy of Sciences USA, vol. 104, no. 2, pp. 501-506, Jan. 2007.
4. U. Singh, E. Bongcam-Rudloff, and B. Westermark, "A DNA Sequence Directed Mutual Transcription Regulation of HSF1 and NFIX Involves Novel Heat Sensitive Protein Interactions," PLoS One, vol. 4, no. 4, e5050, pp. 1-12, 2009.
5. D. Ucar et al., "Predicting Functionality of Protein-DNA Interactions by Integrating Diverse Evidence," Bioinformatics, vol. 25, no. 12, pp. i137-i144, June 2009.
6. J.M. Vaquerizas et al., "A Census of Human Transcription Factors: Function, Expression and Evolution," Nature Rev. Genetics, vol. 10, no. 4, pp. 252-263, Apr. 2009.
7. A. Hoglund and O. Kohlbacher, "From Sequence to Structure and Back Again: Approaches for Predicting Protein-DNA Binding," Proteome Science, vol. 2, no. 1, pp. 1-9, June 2004.
8. Y. Fang et al., "Predicting DNA-Binding Proteins: Approached from Chou's Pseudo Amino Acid Composition and Other Specific Sequence Features," Amino Acids, vol. 34, no. 1, pp. 103-109, Jan. 2008.
9. L. Nanni and A. Lumini, "Combing Ontologies and Dipeptide Composition for Predicting DNA-Binding Proteins," Amino Acids, vol. 34, no. 4, pp. 635-641, May 2008.
10. V.H. Nagaraj, R.A. O'Flanagan, and A.M. Sengupta, "Better Estimation of Protein-DNA Interaction Parameters Improve Prediction of Functional Sites," BMC Biotechnology, vol. 8, article 94, 2008.
11. P. Aloy et al., "Automated Structure-Based Prediction of Functional Sites in Proteins: Applications to Assessing the Validity of Inheriting Protein Function from Homology in Genome Annotation and to Protein Docking," J. Molecular Biology, vol. 311, no. 2, pp. 395-408, Aug. 2001.
12. N. Bhardwaj et al., "Structure Based Prediction of Binding Residues on DNA-Binding Proteins," Proc. IEEE 27th Int'l Conf. Eng. in Medicine and Biology Soc., vol. 3, pp. 2611-4, 2005.
13. S. Jones et al., "Using Electrostatic Potentials to Predict DNABinding Sites on DNA-Binding Proteins," Nucleic Acids Research, vol. 31, no. 24, pp. 7189-98, Dec. 2003.
14. I.B. Kuznetsov et al., "Using Evolutionary and Structural Information to Predict DNA-Binding Sites on DNA-Binding Proteins," Proteins, vol. 64, no. 1, pp. 19-27, July 2006.
15. G. Nimrod et al., "Identification of DNA-Binding Proteins Using Structural, Electrostatic and Evolutionary Features," J. Molecular Biology, vol. 387, no. 4, pp. 1040-1053, Apr. 2009.
16. G. Nimrod et al., "iDBPs: A Web Server for the Identification of DNA Binding Proteins," Bioinformatics, vol. 26, no. 5, pp. 692-693, Mar. 2010.
17. E.W. Stawiski, L.M. Gregoret, and Y. Mandel-Gutfreund, "Annotating Nucleic Acid-Binding Function Based on Protein Structure," J. Molecular Biology, vol. 326, no. 4, pp. 1065-1079, Feb. 2003.
18. S. Ahmad and A. Sarai, "PSSM-Based Prediction of DNA Binding Sites in Proteins," BMC Bioinformatics, vol. 6, article 33, 2005.
19. L. Wang and S.J. Brown, "Prediction of DNA-Binding Residues from Sequence Features," J. Bioinformatics Computational Biology, vol. 4, no. 6, pp. 1141-1158, Dec. 2006.
20. L. Wang and S.J. Brown, "BindN: A Web-Based Tool for Efficient Prediction of DNA and RNA Binding Sites in Amino Acid Sequences," Nucleic Acids Research, vol. 34, no. web server issue, pp. W243-W248, July 2006.
21. C. Yan et al., "Predicting DNA-Binding Sites of Proteins from Amino Acid Sequence," BMC Bioinformatics, vol. 7, article 262, 2006.
22. N. Bhardwaj and H. Lu, "Residue-Level Prediction of DNABinding Sites and Its Application on DNA-Binding Protein Predictions," FEBS Letters, vol. 581, no. 5, pp. 1058-1066, Mar. 2007.
23. S. Hwang, Z. Gou, and I.B. Kuznetsov, "DP-Bind: A Web Server for Sequence-Based Prediction of DNA-Binding Residues in DNABinding Proteins," Bioinformatics, vol. 23, no. 5, pp. 634-636, Mar. 2007.
24. Y. Ofran, V. Mysore, and B. Rost, "Prediction of DNA-Binding Residues from Sequence," Bioinformatics, vol. 23, no. 13, pp. i347-i353, July 2007.
25. H. Tjong and H.X. Zhou, "DISPLAR: An Accurate Method for Predicting DNA-Binding Sites on Protein Surfaces," Nucleic Acids Research, vol. 35, no. 5, pp. 1465-1477, 2007.
26. Y.F. Huang et al., "DNA-Binding Residues and Binding Mode Prediction with Binding-Mechanism Concerned Models," BMC Genomics, vol. 10, Suppl. 3, article S23, pp. 1-10, 2009.
27. L. Wang, M.Q. Yang, and J.Y. Yang, "Prediction of DNA-Binding Residues from Protein Sequence Information Using Random Forests," BMC Genomics, vol. 10, Suppl. 1, article S1, pp. 1-9, 2009.
28. J.-S. Wu, X. Ma, H.-D. Liu, X.-N. Yang, J.-M. Xie, and X. Sun, "A SVM-Based Approach for Predicting DNA-Binding Residues in Proteins from Amino Acid Sequences," Proc. Int'l Joint Conf. Bioinformatics, Systems Biology and Intelligent Computing, pp. 225-229, 2009.
29. L. Wang et al., "BindN+ for Accurate Prediction of DNA and RNA-Binding Residues from Protein Sequence Features," BMC Systems Biology, vol. 4, Suppl 1, article S3, pp. 1-9, 2010.
30. S. Ahmad, M.M. Gromiha, and A. Sarai, "Analysis and Prediction of DNA-Binding Proteins and Their Binding Residues Based on Composition, Sequence and Structural Information," Bioinformatics, vol. 20, no. 4, pp. 477-486, Mar. 2004.
31. J. Si et al., "MetaDBSite: A Meta Approach to Improve Protein DNA-Binding Sites Prediction," BMC Systems Biology, vol. 5, Suppl 1, article S7, pp. 1-7, 2011.
32. H.M. Berman et al., "The Protein Data Bank," Nucleic Acids Research, vol. 28, no. 1, pp. 235-242, Jan. 2000.
33. S.F. Altschul et al., "Basic Local Alignment Search Tool," J. Molecular Biology, vol. 215, no. 3, pp. 403-410, Oct. 1990.
34. S.F. Altschul et al., "Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs," Nucleic Acids Research, vol. 25, no. 17, pp. 3389-3402, Sept. 1997.
35. Q. Zhang, S. Yoon, and W.J. Welsh, "Improved Method for Predicting Beta-Turn Using Support Vector Machine," Bioinformatics, vol. 21, no. 10, pp. 2370-2374, May 2005.
36. J. Wang, "Biochemistry," Higher Education (in Chinese), 2002.
37. V. Veljkovic et al., "Application of the EIIP/ISM Bioinformatics Concept in Development of New Drugs," Current Medical Chemistry, vol. 14, no. 4, pp. 441-453, 2007.
38. D. Bonchev, "The Overall Wiener Index-A New Tool for Characterization of Molecular Topology," J. Chemical Information and Computer Sciences, vol. 41, no. 3, pp. 582-592, May/June 2001.
39. V.N. Vapnik, Statisical Learning Theory. Wiley, 1998.
40. L.J. Hu, Xiu zhen, "Statistical Analysis of Application of Hydrophilicity Hydrophobicity and Molecular Size of Amino Acid (in Chinese)," J. Inner Mongolia Polytechnic Univ., vol. 19, no. 3, pp. 187-191, 2000.
41. J. Shen et al., "Predicting Protein-Protein Interactions Based Only on Sequences Information," Proc. Nat'l Academy of Sciences USA, vol. 104, no. 11, pp. 4337-4341, Mar. 2007.
42. L. Breiman, "Random Forests," Machine Learning, vol. 45, pp. 5-32, 2001.
43. A.W. Liaw and M. Weiner, "Classification and Regression by Random Forest," R. News, vol. 2, pp. 18-22, 2002.
44. G. Cohen et al., "Learning from Imbalanced Data in Surveillance of Nosocomial Infection," Artificial Intelligence Medicine, vol. 37, no. 1, pp. 7-18, May 2006.
45. J.P. Egan, Signal Detection Theory and ROC-Analysis. Academic Press, 1975.
46. A.P. Bradley, "The Use of the Area Under the ROC Curve in the Evaluation of Machine Learning Algorithms," Pattern Recognition, vol. 30, pp. 1145-1159, 1997.
47. W.L. DeLano, The PyMOL Molecular Graphics System. DeLano Scientific, 2002.
48. V. Veljkovic, A Theoretical Approach to Preselection of Carcinogens and Chemical Carcinogenesis. Gordon & Breach, 1980.
49. N. Veljkovic et al., "Discovery of New Therapeutic Targets by the Informational Spectrum Method," Current Protein Peptide Sciences, vol. 9, no. 5, pp. 493-506, Oct. 2008.