DNABINDPROT: Fluctuation-based predictor of DNA-binding residues within a network of interacting residues

Nucleic Acids Research

Volumn 38, Issue SUPPL. 2, 2010, Pages

  Ozbek, Pemra ^a   Soner, Seren ^a   Erman, Burak ^b   Haliloglu, Turkan ^a  

^a BOGAZICI UNIVERSITY   (Turkey)

^b KOÇ UNIVERSITY   (Turkey)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; CYCLIC AMP BINDING PROTEIN; DNA BINDING PROTEIN;

ACCURACY; ARTICLE; BINDING KINETICS; BINDING SITE; BIOINFORMATICS; CLIENT SERVER APPLICATION; DNA BINDING; ESCHERICHIA COLI; NONHUMAN; NORMAL DISTRIBUTION; PREDICTION; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SENSITIVITY AND SPECIFICITY; CHEMISTRY; COMPUTER PROGRAM; INTERNET;

BINDING SITES; CYCLIC AMP RECEPTOR PROTEIN; DNA-BINDING PROTEINS; INTERNET; SOFTWARE;

EID: 77954297726     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq396     Document Type: Article

References (49)

1. Ahmad, S. and Sarai, A. (2004) Moment-based prediction of DNA-binding proteins. J. Mol. Biol., 341, 65-71.
2. Bhardwaj, N., Langlois, R.E., Zhao, G.J. and Lu, H. (2005) Kernel-based machine learning protocol for predicting DNA-binding proteins. Nucleic Acids Res., 33, 6486-6493.
3. Stawiski, E.W., Gregoret, L.M. and Mandel-Gutfreund, Y. (2003) Annotating nucleic acid-binding function based on protein structure. J. Mol. Biol., 326, 1065-1079.
4. Szilagyi, A. and Skolnick, J. (2006) Efficient prediction of nucleic acid binding function from low-resolution protein structures. J. Mol. Biol., 358, 922-933.
5. Gao, M. and Skolnick, J. (2008) DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions. Nucleic Acids Res., 36, 3978-3992.
6. Yan, C., Terribilini, M., Wu, F., Jernigan, R.L., Dobbs, D. and Honavar, V. (2006) Predicting DNA-binding sites of proteins from amino acid sequence. BMC Bioinformatics, 7, 262.
7. Ofran, Y. and Rost, B. (2006) ISIS: interaction sites identified from sequence. Bioinformatics, 23, e13-e16.
8. Ofran, Y., Mysore, V. and Rost, B. (2007) Prediction of DNA-binding residues from sequence. Bioinformatics, 23, i347-i353.
9. Res, I., Mihalek, I. and Lichtarge, O. (2005) An evolution based classifier for prediction of protein interfaces without using protein structures. Bioinformatics, 21, 2496-2501.
10. Wang, B., Chen, P., Huang, D., Li, J., Lok, T. and Lyu, M. (2005) Predicting protein interaction sites from residue spatial sequence profile and evolution rate. FEBS Lett., 580, 380-384.
11. Wang, L., Yang, M.Q. and Yang, J.Y. (2009) Prediction of DNA-binding residues from protein sequence information using random forests. BMC Genomics, 10(Suppl 1), S1.
12. Wu, J., Liu, H., Duan, X., Ding, Y., Wu, H., Bai, Y. and Sun, X. (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.
13. Hwang, S., Gou, Z. and Kuznetsov, I.B. (2007) DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins. Bioinformatics, 23, 634-636.
14. Tsuchiya, Y., Kinoshita, K. and Nakamura, H. (2004) Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces. Proteins, 55, 885-894.
15. Tsuchiya, Y., Kinoshita, K. and Nakamura, H. (2005) PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces. Bioinformatics, 21, 1721-1723.
16. Tjong, H. and Zhou, H.-X. (2007) DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Nucleic Acids Res., 35, 1465-1477.
17. Ahmad, S., Gromiha, M.M. and 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.
18. Keil, M., Exner, T.E. and Brickmann, J. (2004) Pattern recognition strategies for molecular surfaces: III. Binding site prediction with a neural network. J. Comput. Chem, 25, 779-789.
19. Ahmad, S. and Sarai, A. (2005) PSSM based prediction of DNA-binding sites in proteins. BMC Bioinformatics, 6, 33.
20. Kuznetsov, I.B., Gou, Z., Li, R. and Hwang, S. (2006) Using evolutionary and structural information to predict DNA-binding sites on DNA-binding proteins. Proteins, 64, 19-27.
21. Chu, W., Huang, Y., Huang, C., Cheng, Y., Huang, C. and Oyang, Y. (2009) ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors. Nucleic Acids Res., 37, W396-W401.
22. Wang, L. and Brown, S.J. (2006) BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. Nucleic Acids Res., 34, W243-W248.
23. Gao, M. and Skolnick, J. (2009) From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions. PLoS Comput. Biol., 5, e1000341.
24. Gao, M. and Skolnick, J. (2009) A threading-based method for the prediction of DNA-binding proteins with application to the human genome. PLoS Comput. Biol., 5, e1000567.
25. Jones, S., van Heyningen, P., Berman, H.M. and Thornton, J.M. (1999) Protein-DNA interactions: a structural analysis. J. Mol. Biol., 287, 877-896.
26. Sathyapriya, R., Vijayabaskar, M.S. and Saraswathi, V. (2008) Insights into protein-DNA interactions through structure network analysis. PLoS Comput. Biol., 4, e1000170.
27. Lejeune, D., Delsaux, N., Charloteaux, B., Thomas, A. and Brasseur, R. (2005) Protein-nucleic acid recognition: statistical analysis of atomic interactions and influence of DNA structure. Proteins, 61, 258-271.
28. Luscombe, N.M., Laskowski, R.A. and Thornton, J.M. (2001) Amino acid-base interactions: a three dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res., 29, 2860-2874.
29. Luscombe, N.M. and Thornton, J.M. (2002) Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specifity. J. Mol. Biol., 320, 991-1009.
30. Panchenko, A.R., Kondrashov, F. and Bryant, S. (2004) Prediction of functional sites by analysis of sequence and structure conservation. Protein Sci., 13, 884-892.
31. Nimrod, G., Glaser, F., Steinberg, D., Ben-Tal, N. and Pupko, T. (2005) In silico identification of functional regions in proteins. Bioinformatics, 21, i328-i337.
32. Nimrod, G., Schushan, M., Steinberg, D.M. and Ben-Tal, N. (2008) Detection of functionally important regions in 'hypothetical proteins' of known structure. Structure, 16, 1755-1763.
33. Nimrod, G., Szilagyi, A., Leslie, C. and Ben-Tal, N. (2009) Identification of DNA-binding Proteins using structural, electrostatic and evolutionary features. J. Mol. Biol., 387, 1040-1053.
34. Haliloglu, T., Bahar, I. and Erman, B. (1997) Gaussian dynamics of folded proteins, Phys. Rev. Lett., 79, 3090.
35. Bahar, I., Atilgan, A.R. and Erman, B. (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des., 2, 173.
36. Bahar, I., Atilgan, A.R., Demirel, M.C. and Erman, B. (1998) Vibrational dynamics of folded proteins: significance of slow and fast motions in relation to function and stability, Phys. Rev. Lett., 80, 2733-2736.
37. Haliloglu, T., Seyrek, E. and Erman, B. (2008) Prediction of binding sites in receptor-ligand complexes with the Gaussian network model. Phys. Rev. Lett., 100, 228102.
38. Haliloglu, T., Keskin, O., Ma, B. and Nussinov, R. (2005) How similar are protein folding and protein binding nuclei? Examination of fluctuations of energy hot spots and conserved residues. Biophys. J., 88, 1552-1559.
39. Ertekin, A., Nussinov, R. and Haliloglu, T. (2006) Association of putative protein binding sites with the fluctuation behavior of residues. Protein Sci., 15, 2265-2277.
40. Rader, A.J. and Bahar, I. (2004) Folding core predictions from network models of proteins. Polymer, 45, 659-668.
41. Haliloglu, T. and Erman, B. (2009) Analysis of correlations between energy and residue fluctuations in native proteins and determination of specific sites for binding. Phys. Rev. Lett, 102, 088103.
42. Landau, M., Mayrose, I., Rosenberg, Y., Glaser, F., Martz, E., Pupko, T. and Ben-Tal, N. (2005) ConSurf: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res., 33, W299-W302.
43. Laskowski, R.A. (2007) Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature. Bioinformatics, 23, 1824-1827.
44. Luscombe, N.M., Laskowski, R.A. and Thornton, J.M. (1997) NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions. Nucleic Acids Res., 25, 4940-4945.
45. van Dijk, M. and Bonvin, A.M.J.J. (2008) A protein-DNA docking benchmark. Nucleic Acids Res., 36, e88.
46. Wang, G. and Dunbrack, R.L. Jr. (2003) PISCES: a protein sequence culling server. Bioinformatics, 19, 1589-1591.
47. Passner, J.M. and Steitz, T.A. (1997) The structure of a CAP-DNA complex having two cAMP molecules bound to each monomer. Proc Natl. Acad Sci USA, 94, 2843-2847.
48. Passner, J.M., Schultz, S.C. and Steitz, T.A. (2000) Modeling the cAMP-induced allosteric transition using the crystal structure of CAP-cAMP at 2.1A resolution. J. Mol. Biol., 304, 847-859.
49. Popovych, N., Tzeng, S.R., Tonelli, M., Ebright, R.H. and Kalodimos, C.G. (2009) Structural basis for cAMP-mediated allosteric control of the catabolite activator protein. Proc. Natl Acad. Sci. USA, 106, 6927-6932.