title: MetaDBSite: a meta approach to improve protein DNA-binding sites prediction.
abstract: BACKGROUND
  Protein-DNA interactions play an important role in many fundamental biological activities such as DNA replication, transcription and repair. Identification of amino acid residues involved in DNA binding site is critical for understanding of the mechanism of gene regulations. In the last decade, there have been a number of computational approaches developed to predict protein-DNA binding sites based on protein sequence and/or structural information.
  
  
  RESULTS
  In this article, we present metaDBSite, a meta web server to predict DNA-binding residues for DNA-binding proteins. MetaDBSite integrates the prediction results from six available online web servers: DISIS, DNABindR, BindN, BindN-rf, DP-Bind and DBS-PRED and it solely uses sequence information of proteins. A large dataset of DNA-binding proteins is constructed from the Protein Data Bank and it serves as a gold-standard benchmark to evaluate the metaDBSite approach and the other six predictors.
  
  
  CONCLUSIONS
  The comparison results show that metaDBSite outperforms single individual approach. We believe that metaDBSite will become a useful and integrative tool for protein DNA-binding residues prediction. The MetaDBSite web-server is freely available at http://projects.biotec.tu-dresden.de/metadbsite/ and http://sysbio.zju.edu.cn/metadbsite.
authors.affiliation: Systems Biology Division, Zhejiang-California International NanoSystems Institute, Zhejiang University, Kaixuan Road 268, Hangzhou, China.
authors.forename: Jingna
authors.initials: J
authors.lastname: Si
authors.forename: Zengming
authors.initials: Z
authors.lastname: Zhang
authors.forename: Biaoyang
authors.initials: B
authors.lastname: Lin
authors.forename: Michael
authors.initials: M
authors.lastname: Schroeder
authors.forename: Bingding
authors.initials: B
authors.lastname: Huang
mesh_terms: D000595:Amino Acid Sequence; D019985:Benchmarking; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D030562:Databases, Protein; D020407:Internet; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA