title: Structure-based modeling of protein: DNA specificity.
abstract: Protein:DNA interactions are essential to a range of processes that maintain and express the information encoded in the genome. Structural modeling is an approach that aims to understand these interactions at the physicochemical level. It has been proposed that structural modeling can lead to deeper understanding of the mechanisms of protein:DNA interactions, and that progress in this field can not only help to rationalize the observed specificities of DNA-binding proteins but also to allow researchers to engineer novel DNA site specificities. In this review we discuss recent developments in the structural description of protein:DNA interactions and specificity, as well as the challenges facing the field in the future.
authors.forename: Adam P
authors.initials: AP
authors.lastname: Joyce
authors.forename: Chi
authors.initials: C
authors.lastname: Zhang
authors.forename: Philip
authors.initials: P
authors.lastname: Bradley
authors.forename: James J
authors.initials: JJ
authors.lastname: Havranek
mesh_terms: D000818:Animals; D001483:Base Sequence; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D013329:Structure-Activity Relationship; D014867:Water / Q000737:chemistry
chemical_list: D004268:DNA-Binding Proteins; D014867:Water; D004247:DNA
keywords: Binding specificity; Molecular modeling; Protein:DNA interactions; Structural modeling; Structure prediction; Transcription factor binding sites