title: Specificity, free energy and information content in protein-DNA interactions.
abstract: Site-specific DNA-protein interactions can be studied using experimental and computational methods. Experimental approaches typically analyze a protein-DNA interaction by measuring the free energy of binding under a variety of conditions. Computational methods focus on alignments of known binding sites for a protein, and, from these alignments, make estimates of the binding energy. Understanding the relationship between these two perspectives, and finding ways to improve both, is a major challenge of modern molecular biology.
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder 80309-0347, USA. Stormo@Colorado.Edu
authors.forename: G D
authors.initials: GD
authors.lastname: Stormo
authors.forename: D S
authors.initials: DS
authors.lastname: Fields
mesh_terms: D001665:Binding Sites; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D004735:Energy Transfer; D005544:Forecasting; D008956:Models, Chemical; D011485:Protein Binding; D012097:Repressor Proteins / Q000737:chemistry / Q000378:metabolism; D013379:Substrate Specificity; D014158:Transcription, Genetic; D014764:Viral Proteins / Q000737:chemistry / Q000378:metabolism; D054334:Viral Regulatory and Accessory Proteins
chemical_list: D004268:DNA-Binding Proteins; D012097:Repressor Proteins; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins; D004247:DNA