Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome

PLoS ONE

Volumn 9, Issue 5, 2014, Pages

  Zhao, Huiying ^a,b,c   Wang, Jihua ^b,d   Zhou, Yaoqi ^a,b,d,e   Yang, Yuedong ^a,b,e  

^a INDIANA UNIVERSITY   (United States)

^b INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c QIMR BERGHOFER MEDICAL RESEARCH INSTITUTE   (Australia)

^d DEZHOU UNIVERSITY   (China)

^e GRIFFITH UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; DNA; PROTEIN BINDING; PROTEOME;

ACCURACY; AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; BINDING AFFINITY; BIOINFORMATICS; COMPLEX FORMATION; COMPUTER PREDICTION; CONTROLLED STUDY; CORRELATION COEFFICIENT; DNA PROTEIN COMPLEX; FALSE POSITIVE RESULT; INTERMETHOD COMPARISON; KNOWLEDGE BASE; NUCLEOTIDE SEQUENCE; PERFORMANCE MEASUREMENT SYSTEM; PROTEIN DATABASE; PROTEIN DETERMINATION; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN STRUCTURE; PROTEOMICS; RESIDUE ANALYSIS; SENSITIVITY ANALYSIS; STRUCTURE ANALYSIS; VALIDATION STUDY; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; METABOLISM; PROCEDURES; PROTEIN CONFORMATION;

BINDING SITES; DATABASES, PROTEIN; DNA; DNA-BINDING PROTEINS; HUMANS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEOME; PROTEOMICS;

EID: 84900403851     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0096694     Document Type: Article

References (67)

1. Apweiler R, Martin MJ, O'Donovan C, Magrane M, Alam-Faruque Y, et al. (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Research 38: D142-D148.
2. Engelhardt BE, Jordan MI, Srouji JR, Brenner SE (2011) Genome-scale phylogenetic function annotation of large and diverse protein families. Genome Res 21: 1969-1980.
3. Stawiski EW, Gregoret LM, Mandel-Gutfreund Y (2003) Annotating nucleic acid-binding function based on protein structure. Journal of Molecular Biology 326: 1065-1079. (Pubitemid 36263383)
4. Cai YD, Lin SL (2003) Support vector machines for predicting rRNA-, RNA-, and DNA-binding proteins from amino acid sequence. Biochimica Et Biophysica Acta-Proteins and Proteomics 1648: 127-133.
5. Jones S, Barker JA, Nobeli I, Thornton JM (2003) Using structural motif templates to identify proteins with DNA binding function. Nucleic Acids Research 31: 2811-2823. (Pubitemid 37442125)
6. Ahmad S, Gromiha MM, Sarai A (2004) Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information. Bioinformatics 20: 477-486. (Pubitemid 38344327)
7. Ahmad S, Sarai A (2004) Moment-based prediction of DNA-binding proteins. Journal of Molecular Biology 341: 65-71. (Pubitemid 39090635)
8. Bhardwaj N, Langlois RE, Zhao GJ, Lu H (2005) Kernel-based machine learning protocol for predicting DNA-binding proteins. Nucleic Acids Research 33: 6486-6493. (Pubitemid 41806412)
9. Bhardwaj N, Lu H (2007) Residue-level prediction of DNA-binding sites and its application on DNA-binding protein predictions. Febs Letters 581: 1058-1066. (Pubitemid 46282728)
10. Lin WZ, Fang JA, Xiao X, Chou KC (2011) iDNA-Prot: Identification of DNA Binding Proteins Using Random Forest with Grey Model. PLoS One 6: e24756.
11. Yang YD, Zhan J, Zhao HY, Zhou YQ (2012) A new size-independent score for pairwise protein structure alignment and its application to structure classification and nucleic-acid binding prediction. Proteins-Structure Function and Bioinformatics 80: 2080-2088.
12. Kumar M, Gromiha MM, Raghava GP (2007) Identification of DNA-binding proteins using support vector machines and evolutionary profiles. BMC Bioinformatics 8: 463.
13. Nimrod G, Schushan M, Szilagyi A, Leslie C, Ben-Tal N (2010) iDBPs: a web server for the identification of DNA binding proteins. Bioinformatics 26: 692-693.
14. Langlois RE, Lu H (2010) Boosting the prediction and understanding of DNA-binding domains from sequence. Nucleic Acids Research 38: 3149-3158.
15. Huang HL, Lin IC, Liou YF, Tsai CT, Hsu KT, et al. (2011) Predicting and analyzing DNA-binding domains using a systematic approach to identifying a set of informative physicochemical and biochemical properties. BMC Bioinformatics 12: S47.
16. Zhou WQ, Yan H (2011) Prediction of DNA-binding protein based on statistical and geometric features and support vector machines. Proteome Science 9: S1.
17. Szilagyi A, Skolnick J (2006) Efficient prediction of nucleic acid binding function from low-resolution protein structures. Journal of Molecular Biology 358: 922-933.
18. Yu XJ, Cao JP, Cai YD, Shi TL, Li YX (2006) Predicting rRNA-, RNA-, and DNA-binding proteins from primary structure with support vector machines. Journal of Theoretical Biology 240: 175-184.
19. Nimrod G, Szilagyi A, Leslie C, Ben-Tal N (2009) Identification of DNA-binding Proteins Using Structural, Electrostatic and Evolutionary Features. Journal of Molecular Biology 387: 1040-1053.
20. Kumar KK, Pugalenthi G, Suganthan PN (2009) DNA-Prot: Identification of DNA Binding Proteins from Protein Sequence Information using Random Forest. Journal of Biomolecular Structure & Dynamics 26: 679-686.
21. Jones S, Shanahan HP, Berman HM, Thornton JM (2003) Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. Nucleic Acids Research 31: 7189-7198. (Pubitemid 38008449)
22. Ahmad S, Sarai A (2005) PSSM-based prediction of DNA binding sites in proteins. BMC Bioinformatics 6: 33.
23. Tsuchiya Y, Kinoshita K, Nakamura H (2005) PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces. Bioinformatics 21: 1721-1723. (Pubitemid 40542743)
24. Tjong H, Zhou HX (2007) DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Nucleic Acids Res 35: 1465-1477. (Pubitemid 46592869)
25. Hwang S, Gou Z, Kuznetsov IB (2007) DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins. Bioinformatics 23: 634-636. (Pubitemid 46522600)
26. Xiong Y, Xia J, Zhang W, Liu J (2011) Exploiting a reduced set of weighted average features to improve prediction of DNA-binding residues from 3D structures. PLoS One 6: e28440.
27. Chen YC, Wright JD, Lim C (2012) DR-bind: a web server for predicting DNA-binding residues from the protein structure based on electrostatics, evolution and geometry. Nucleic Acids Research 40: W249-W256.
28. Dey S, Pal A, Guharoy M, Sonavane S, Chakrabarti P (2012) Characterization and prediction of the binding site in DNA-binding proteins: improvement of accuracy by combining residue composition, evolutionary conservation and structural parameters. Nucleic Acids Res 40: 7150-7161.
29. Comin M, Guerra C, Dellaert F (2009) Binding Balls: Fast Detection of Binding Sites Using a Property of Spherical Fourier Transform. Journal of Computational Biology 16: 1577-1591.
30. Konc J, Janezic D (2010) ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment. Bioinformatics 26: 1160-1168.
31. Wang LJ, Huang CY, Yang MQ, Yang JY (2010) BindN plus for accurate prediction of DNA and RNA-binding residues from protein sequence features. Bmc Systems Biology 4: S3.
32. Ozbek P, Soner S, Erman B, Haliloglu T (2010) DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues. Nucleic Acids Research 38: W417-W423.
33. Carson MB, Langlois R, Lu H (2010) NAPS: a residue-level nucleic acid-binding prediction server. Nucleic Acids Res 38: W431-435.
34. Cai YD, He ZS, Shi XH, Kong XY, Gu L, et al. (2010) A Novel Sequence-Based Method of Predicting Protein DNA-Binding Residues, Using a Machine Learning Approach. Molecules and Cells 30: 99-105.
35. Xiong Y, Liu JA, Wei DQ (2011) An accurate feature-based method for identifying DNA-binding residues on protein surfaces. Proteins-Structure Function and Bioinformatics 79: 509-517.
36. Si JN, Zhang ZM, Lin BY, Schroeder M, Huang BD (2011) MetaDBSite: a meta approach to improve protein DNA-binding sites prediction. Bmc Systems Biology 5: S7.
37. Yan CH, Terribilini M, Wu FH, Jernigan RL, Dobbs D, et al. (2006) Predicting DNA-binding sites of proteins from amino acid sequence. BMC Bioinformatics 7: 262.
38. Kuznetsov IB, Gou ZK, Li R, Hwang SW (2006) Using evolutionary and structural information to predict DNA-binding sites on DNA-binding proteins. Proteins-Structure Function and Bioinformatics 64: 19-27. (Pubitemid 43830981)
39. Wang LJ, Brown SJ (2006) BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. Nucleic Acids Research 34: W243-W248.
40. Contreras-Moreira B, Collado-Vides J (2006) Comparative footprinting of DNA-binding proteins. Bioinformatics 22: E74-E80. (Pubitemid 44288275)
41. Wang LJ, Yang MQ, Yang JY (2009) Prediction of DNA-binding residues from protein sequence information using random forests. BMC Genomics 10: S1.
42. Wu JS, Liu HD, Duan XY, Ding Y, Wu HT, et al. (2009) Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature. Bioinformatics 25: 30-35.
43. Gao M, Skolnick J (2009) From Nonspecific DNA-Protein Encounter Complexes to the Prediction of DNA-Protein Interactions. Plos Computational Biology 5: E1000341.
44. Andrabi M, Mizuguchi K, Sarai A, Ahmad S (2009) Prediction of mono- and dinucleotide-specific DNA-binding sites in proteins using neural networks. Bmc Structural Biology 9: 30.
45. Frech K, Herrmann G, Werner T (1993) Computer-Assisted Prediction, Classification, and Delimitation of Protein-Binding Sites in Nucleic-Acids. Nucleic Acids Research 21: 1655-1664. (Pubitemid 23146335)
46. Aloy P, Querol E, Aviles FX, Sternberg MJ (2001) 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. Journal of Molecular Biology 311: 395-408. (Pubitemid 32744549)
47. Gao M, Skolnick J (2008) DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions. Nucleic Acids Research 36: 3978-3992. (Pubitemid 351984814)
48. Gao M, Skolnick J (2009) A Threading-Based Method for the Prediction of DNA-Binding Proteins with Application to the Human Genome. PLOS Computational Biology 5: E1000567.
49. Skolnick J, Kihara D, Zhang Y (2004) Development and large scale benchmark testing of the PROSPECTOR-3 threading algorithm. Proteins-Structure Function and Bioinformatics 56: 502-518. (Pubitemid 38924963)
50. Zhou HY, Zhou Y (2002) Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Science 11: 2714-2726.
51. Xu BS, Yang YD, Liang HJ, Zhou YQ (2009) An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles. Proteins-Structure Function and Bioinformatics 76: 718-730.
52. Zhang C, Liu S, Zhu QQ, Zhou YQ (2005) A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. Journal of Medicinal Chemistry 48: 2325-2335. (Pubitemid 40516427)
53. Zhao HY, Yang YD, Zhou YQ (2010) Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function. Bioinformatics 26: 1857-1863.
54. Remmert M, Biegert A, Hauser A, Soding J (2012) HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nature methods 9: 173-175.
55. Yang Y, Faraggi E, Zhao H, Zhou Y (2011) Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of the query and corresponding native properties of templates. Bioinformatics 27: 2076-2082.
56. Mariani V, Kiefer F, Schmidt T, Haas J, Schwede T (2011) Assessment of template based protein structure predictions in CASP9. Proteins-Structure Function and Bioinformatics 79 Suppl 10: 37-58.
57. Zhao H, Yang Y, Zhou Y (2011) Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction. RNA Biology 8: 988-996.
58. Zhao H, Yang Y, Zhou Y (2011) Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets. Nucleic Acids Res 39: 3017-3025.
59. Zhao H, Yang Y, Janga SC, Kao C, Zhou Y (2013) Prediction and validation of the unexplored RNA-binding protein atlas of the human proteome. Proteins: 82, 640-647 (2014).
60. Nowotny M, Gaidamakov SA, Ghirlando R, Cerritelli SM, Crouch RJ, et al. (2007) Structure of human RNase h1 complexed with an RNA/DNA hybrid: Insight into HIV reverse transcription. Molecular Cell 28: 264-276. (Pubitemid 47599996)
61. Muller CW, Rey FA, Sodeoka M, Verdine GL, Harrison SC (1995) Structure of the NF-kappa B p50 homodimer bound to DNA. Nature 373: 311-317.
62. Luo DH, Xu T, Watson RP, Scherer-Becker D, Sampath A, et al. (2008) Insights into RNA unwinding and ATP hydrolysis by the flavivirus NS3 protein. Embo Journal 27: 3209-3219.
63. Xu T, Sampath A, Chao A, Wen DY, Nanao M, et al. (2005) Structure of the Dengue virus helicase/nucleoside triphosphatase catalytic domain at a resolution of 2.4 angstrom. Journal of Virology 79: 10278-10288. (Pubitemid 41098569)
64. Botstein D, Ashburner M, Ball CA, Blake JA, Butler H, et al. (2000) Gene Ontology: tool for the unification of biology. Nature Genetics 25: 25-29. (Pubitemid 30257031)
65. Nilsen H, Otterlei M, Haug T, Solum K, Nagelhus TA, et al. (1997) Nuclear and mitochondrial uracil-DNA glycosylases are generated by alternative splicing and transcription from different positions in the UNG gene. Nucleic Acids Res 25: 750-755. (Pubitemid 27299828)
66. Sladek R, Beatty B, Squire J, Copeland NG, Gilbert DJ, et al. (1997) Chromosomal mapping of the human and murine orphan receptors ERRalpha (ESRRA) and ERRbeta (ESRRB) and identification of a novel human ERRalpha-related pseudogene. Genomics 45: 320-326. (Pubitemid 27467622)
67. Sherman BT, Huang DW, Tan QN, Guo YJ, Bour S, et al. (2007) DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. BMC Bioinformatics 8: 426.