title: A structure-based method for identifying DNA-binding proteins and their sites of DNA-interaction.
abstract: A classification model of a DNA-binding protein chain was created based on identification of alpha helices within the chain likely to bind to DNA. Using the model, all chains in the Protein Data Bank were classified. For many of the chains classified with high confidence, previous documentation for DNA-binding was found, yet no sequence homology to the structures used to train the model was detected. The result indicates that the chain model can be used to supplement sequence based methods for annotating the function of DNA-binding. Four new candidates for DNA-binding were found, including two structures solved through structural genomics efforts. For each of the candidate structures, possible sites of DNA-binding are indicated by listing the residue ranges of alpha helices likely to interact with DNA.
authors.affiliation: Department of Chemistry and Chemical Biology, Rutgers-The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA.
authors.forename: William A
authors.initials: WA
authors.lastname: McLaughlin
authors.forename: Daniel W
authors.initials: DW
authors.lastname: Kulp
authors.forename: Joanna
authors.initials: J
authors.lastname: de la Cruz
authors.forename: Xiang-Jun
authors.initials: XJ
authors.lastname: Lu
authors.forename: Catherine L
authors.initials: CL
authors.lastname: Lawson
authors.forename: Helen M
authors.initials: HM
authors.lastname: Berman
mesh_terms: D001665:Binding Sites; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000032:analysis / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D011487:Protein Conformation; D017433:Protein Structure, Secondary
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA