DR-bind: A web server for predicting DNA-binding residues from the protein structure based on electrostatics, evolution and geometry

Nucleic Acids Research

Volumn 40, Issue W1, 2012, Pages

  Chen, Yao Chi ^a   Wright, Jon D ^a,b   Lim, Carmay ^a,c  

^a INSTITUTE OF BIOMEDICAL SCIENCES   (Taiwan)

^b GENOMICS RESEARCH CENTER   (Taiwan)

^c NATIONAL TSING HUA UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; CALIBRATION; COMPUTER PROGRAM; CONTROLLED STUDY; DNA BINDING MOTIF; DNA PROTEIN COMPLEX; GENE MUTATION; GEOMETRY; INTERMETHOD COMPARISON; INTERNET; MACHINE LEARNING; MOLECULAR EVOLUTION; PREDICTION; PRIORITY JOURNAL; PROTEIN STRUCTURE; SENSITIVITY AND SPECIFICITY; STATIC ELECTRICITY; STRUCTURAL GENOMICS; TRAINING; WEB SERVER;

BINDING SITES; DNA-BINDING PROTEINS; EVOLUTION, MOLECULAR; INTERNET; PROTEIN CONFORMATION; SOFTWARE; STATIC ELECTRICITY;

EID: 84864476751     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks481     Document Type: Article

References (44)

1. Strong, M.J., Volkening, K., Hammond, R., Yang, W., Strong, W., Leystra-Lantz, C. and Shoesmith, C. (2007) TDP43 is a human low molecular weight neurofilament (hNFL) mRNA-binding protein. Mol. Cell. Neurosci., 35, 320-327.
2. Pavletich, N.P., Chambers, K.A. and Pabo, C.O. (1993) The DNA-binding domain of p53 contains the four conserved regions and the major mutation hot spots. Genes Dev., 7, 2556-2564.
3. 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.
4. 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.
5. Ahmad, S. and Sarai, A. (2005) PSSM-based prediction of DNA binding sites in proteins. BMC Bioinformatics, 6, 33.
6. Yan, C., Terribilini, M., Wu, F., Jernigan, R., Dobbs, D. and Honavar, V. (2006) Predicting DNA-binding sites of proteins from amino acid sequence. BMC Bioinformatics, 7, 262.
7. 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.
8. 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.
9. Ofran, Y., Mysore, V. and Rost, B. (2007) Prediction of DNA-binding residues from sequence. Bioinformatics, 23, i347-i353.
10. 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.
11. 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.
12. Wang, L., Huang, C., Yang, M. and Yang, J. (2010) BindN+for accurate prediction of DNA and RNA-binding residues from protein sequence features. BMC Syst. Biol., 4, S3.
13. 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.
14. Wang, L., Yang, M.Q. and Yang, J.Y. (2009) Prediction of DNA-binding residues from protein sequence information using random forest. BMC Genomics, 10, S1.
15. Carson, M.B., Langlois, R. and Lu, H. (2010) NAPS: a residue-level nucleic aciD-binding prediction server. Nucleic Acids Res., 38, W431-W435.
16. Si, J., Zhang, Z., Lin, B., Schroeder, M. and Huang, B. (2011) MetaDBSite: a meta approach to improve protein DNA-binding sites prediction. BMC Syst. Biol., 5, S7.
17. 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.
18. 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.
19. 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.
20. Shanahan, H.P., Garcia, M.A., Jones, S. and Thornton, J.M. (2004) Identifying DNA-binding proteins using structural motifs and the electrostatic potential. Nucleic Acids Res., 32, 4732-4741.
21. Ferrer-Costa, C., Shanahan, H.P., Jones, S. and Thornton, J.M. (2005) HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif. Bioinformatics, 21, 3679-3680.
22. Wu, C.Y., Chen, Y.C. and Lim, C. (2010) A structural-alphabet-based strategy for finding structural motifs across protein families. Nucleic Acids Res., 38, e150.
23. Ozbek, P., Soner, S., Erman, B. and Haliloglu, T. (2010) DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues. Nucleic Acids Res., 38, W417-W423.
24. Tsuchiya, Y., Kinoshita, K. and Nakamura, H. (2005) PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces. Bioinformatics, 21, 1721-1723.
25. Tjong, H. and Zhou, H.X. (2007) DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Nucleic Acids Res., 35, 1465.
26. 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.
27. Chen, Y.C., Wu, C.Y. and Lim, C. (2007) Predicting DNA-binding sites on proteins from electrostatic stabilization upon mutation to Asp/Glu and evolutionary conservation. Proteins, 67, 671-680.
28. van Dijk, M. and Bonvin, A.M.J.J. (2008) A protein-DNA docking benchmark. Nucleic Acids Res., 36, e88.
29. Chen, Y.C. and Lim, C. (2008) Common physical basis of macromolecule-binding sites in proteins. Nucleic Acids Res., 36, 7078-7087.
30. Berman, H.M., Battistuz, T., Bhat, T.N., Bluhm, W.F., Bourne, P.E., Burkhardt, K., Iype, L., Jain, S., Fagan, P., Marvin, J. et al. (2002) The protein data bank. Acta Crystallogr. D, 58, 899-907.
31. Pearl, F., Todd, A., Sillitoe, I., Dibley, M., Redfern, O., Lewis, T., Bennett, C., Marsden, R., Grant, A., Lee, D. et al. (2005) The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucleic Acids Res., 33, D247-D251.
32. Goldenberg, O., Erez, E., Nimrod, G. and Ben-Tal, N. (2009) The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures. Nucleic Acids Res., 37, D323-D327.
33. Taylor, W.R. and Orengo, C.A. (1989) Protein structure alignment. J. Mol. Biol., 208, 1-22.
34. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
35. McDonald, I.K. and Thornton, J.M. (1994) Satisfying hydrogen bonding potential in proteins. J. Mol. Biol., 238, 777-793.
36. Miller, S., Janin, J., Lesk, A.M. and Chothia, C. (1987) Interior and surface of monomeric proteins. J. Mol. Biol., 196, 641-656.
37. Koradi, R., Billeter, M. and Wuthrich, K. (1996) MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph., 14, 51-55.
38. Canutescu, A.A., Shelenkov, A.A. and Dunbrack, R.L. Jr (2003) A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci., 12, 2001-2014.
39. Case, D.A., Cheatham, T.E. III, Darden, T., Gohlke, H., Luo, R., Merz, K.M. Jr, Onufriev, A., Simmerling, C., Wang, B. and Woods, R.J. (2005) The Amber biomolecular simulation programs. J. Comput. Chem., 26, 1668-1688.
40. Duan, Y., Wu, C., Chowdhury, S., Lee, M.C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T. et al. (2003) A point-charge force field for molecular mechanics simulations of proteins based on condenseD-phase quantum mechanical calculations. J. Comput. Chem., 24, 1999-2012.
41. Ashkenazy, H., Erez, E., Martz, E., Pupko, T. and Ben-Tal, N. (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res., 38, W529-W533.
42. Landau, M., Mayrose, I., Rosenberg, Y., Glaser, F., Martz, E., Pupko, T. and Ben-Tal, N. (2005) ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res., 33, 299-302.
43. Glaser, F., Pupko, T., Paz, I., Bell, R.E., Bechor-Shental, D., Martz, E. and Ben-Tal, N. (2003) ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics, 19, 163-164.
44. Chen, Y.C. and Lim, C. (2008) Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry. Nucleic Acids Res., 36, e29.