title: OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites.
abstract: We present OnTheFly (http://bhapp.c2b2.columbia.edu/OnTheFly/index.php), a database comprising a systematic collection of transcription factors (TFs) of Drosophila melanogaster and their DNA-binding sites. TFs predicted in the Drosophila melanogaster genome are annotated and classified and their structures, obtained via experiment or homology models, are provided. All known preferred TF DNA-binding sites obtained from the B1H, DNase I and SELEX methodologies are presented. DNA shape parameters predicted for these sites are obtained from a high throughput server or from crystal structures of protein-DNA complexes where available. An important feature of the database is that all DNA-binding domains and their binding sites are fully annotated in a eukaryote using structural criteria and evolutionary homology. OnTheFly thus provides a comprehensive view of TFs and their binding sites that will be a valuable resource for deciphering non-coding regulatory DNA.
authors.affiliation: Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Department of Systems Biology, Center for Computational Biology and Bioinformatics, Columbia University, 1130 St. Nicholas Avenue, New York, NY 10032, USA, Department of Life Science, Open University of Israel, Ra'anana 43107, Israel and Department of Biochemistry and Molecular Biophysics, Columbia University, 701 West 168th Street, HHSC 1104, New York, NY 10032, USA.
authors.forename: Shula
authors.initials: S
authors.lastname: Shazman
authors.forename: Hunjoong
authors.initials: H
authors.lastname: Lee
authors.forename: Yakov
authors.initials: Y
authors.lastname: Socol
authors.forename: Richard S
authors.initials: RS
authors.lastname: Mann
authors.forename: Barry
authors.initials: B
authors.lastname: Honig
mesh_terms: D000818:Animals; D001665:Binding Sites; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D030541:Databases, Genetic; D029721:Drosophila Proteins / Q000737:chemistry / Q000378:metabolism*; D004331:Drosophila melanogaster / Q000235:genetics*; D020407:Internet; D058977:Molecular Sequence Annotation; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D050436:Regulatory Elements, Transcriptional; D012984:Software; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism*
chemical_list: D029721:Drosophila Proteins; D014157:Transcription Factors; D004247:DNA