title: Proteopedia: 3D visualization and annotation of transcription factor-DNA readout modes.
abstract: 3D visualization assists in identifying diverse mechanisms of protein-DNA recognition that can be observed for transcription factors and other DNA binding proteins. We used Proteopedia to illustrate transcription factor-DNA readout modes with a focus on DNA shape, which can be a function of either nucleotide sequence (Hox proteins) or base pairing geometry (p53). © 2012 by The International Union of Biochemistry and Molecular Biology.
authors.affiliation: Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, and Physics and Astronomy, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, USA.
authors.forename: Ana Carolina Dantas
authors.initials: AC
authors.lastname: Machado
authors.forename: Skyler B
authors.initials: SB
authors.lastname: Saleebyan
authors.forename: Bailey T
authors.initials: BT
authors.lastname: Holmes
authors.forename: Maria
authors.initials: M
authors.lastname: Karelina
authors.forename: Julia
authors.initials: J
authors.lastname: Tam
authors.forename: Sharon Y
authors.initials: SY
authors.lastname: Kim
authors.forename: Keziah H
authors.initials: KH
authors.lastname: Kim
authors.forename: Iris
authors.initials: I
authors.lastname: Dror
authors.forename: Eran
authors.initials: E
authors.lastname: Hodis
authors.forename: Eric
authors.initials: E
authors.lastname: Martz
authors.forename: Patricia A
authors.initials: PA
authors.lastname: Compeau
authors.forename: Remo
authors.initials: R
authors.lastname: Rohs
mesh_terms: D000818:Animals; D001671:Biochemistry / Q000193:education* / Q000379:methods; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D018398:Homeodomain Proteins / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D021621:Imaging, Three-Dimensional; D008958:Models, Molecular; D058977:Molecular Sequence Annotation; D016159:Tumor Suppressor Protein p53 / Q000737:chemistry* / Q000378:metabolism
chemical_list: D018398:Homeodomain Proteins; C495901:TP53 protein, human; D016159:Tumor Suppressor Protein p53; D004247:DNA