MetaDBSite: A meta approach to improve protein DNA-binding sites prediction

BMC Systems Biology

Volumn 5, Issue SUPPL. 1, 2011, Pages

  Si, Jingna ^a,c   Zhang, Zengming ^a   Lin, Biaoyang ^a   Schroeder, Michael ^b   Huang, Bingding ^a,b  

^a ZHEJIANG UNIVERSITY   (China)

^b DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

^c CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA BINDING PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; INTERNET; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DATABASE; QUALITY CONTROL;

AMINO ACID SEQUENCE; BENCHMARKING; BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; DNA; DNA-BINDING PROTEINS; INTERNET; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; PROTEIN CONFORMATION;

EID: 79959217445     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-S1-S7     Document Type: Article

References (16)

1. Ptashne M. Regulation of transcription: from lambda to eukaryotes. Trends Biochem Sci 2005, 30:275-279. 10.1016/j.tibs.2005.04.003, 15950866.
2. Ofran Y, Mysore V, Rost B. Prediction of DNA-binding residues from sequence. Bioinformatics 2007, 23:i347-353. 10.1093/bioinformatics/btm174, 17646316.
3. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000, 28:235-242. 10.1093/nar/28.1.235, 102472, 10592235.
4. Yan C, Terribilini M, Wu F, Jernigan RL, Dobbs D, Honavar V. Predicting DNA-binding sites of proteins from amino acid sequence. BMC Bioinformatics 2006, 7:262. 10.1186/1471-2105-7-262, 1534068, 16712732.
5. Wang L, Brown SJ. BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. Nucleic Acids Res 2006, 34:W243-248. 10.1093/nar/gkl298, 1538853, 16845003.
6. Wang L, Yang MQ, Yang JY. Prediction of DNA-binding residues from protein sequence information using random forests. Bmc Genomics 2009, 10(Suppl 1):S1. 10.1186/1471-2164-10-S1-S1, 2709252, 19594868.
7. Hwang S, Gou Z, Kuznetsov IB. DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins. Bioinformatics 2007, 23:634-636. 10.1093/bioinformatics/btl672, 17237068.
8. Ahmad S, Gromiha MM, Sarai A. Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information. Bioinformatics 2004, 20:477-486. 10.1093/bioinformatics/btg432, 14990443.
9. Lv S, Wang X, Cui Y, Jin J, Sun Y, Tang Y, Bai Y, Wang Y, Zhou L. Application of attention network test and demographic information to detect mild cognitive impairment via combining feature selection with support vector machine. Comput Methods Programs Biomed 97:11-18. 10.1016/j.cmpb.2009.05.003, 19500873.
10. Calle ML, Urrea V. Letter to the Editor: Stability of Random Forest importance measures. Brief Bioinform 2010,
11. De Roach JN. Neural networks--an artificial intelligence approach to the analysis of clinical data. Australas Phys Eng Sci Med 1989, 12:100-106.
12. Wang L, Brown SJ. Prediction of DNA-binding residues from sequence features. J Bioinform Comput Biol 2006, 4:1141-1158. 10.1142/S0219720006002387, 17245807.
13. Tsuchiya Y, Kinoshita K, Nakamura H. PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces. Bioinformatics 2005, 21:1721-1723. 10.1093/bioinformatics/bti232, 15613393.
14. Ahmad S, Sarai A. PSSM-based prediction of DNA binding sites in proteins. BMC Bioinformatics 2005, 6:33. 10.1186/1471-2105-6-33, 550660, 15720719.
15. Jones S, Shanahan HP, Berman HM, Thornton JM. Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. Nucleic Acids Res 2003, 31:7189-7198. 10.1093/nar/gkg922, 291864, 14654694.
16. Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22:1658-1659. 10.1093/bioinformatics/btl158, 16731699.