title: An analysis of information content present in protein-DNA interactions.
abstract: Understanding the role proteins play in regulating DNA replication is essential to forming a complete picture of how the genome manifests itself. In this work, we examine the feasibility of predicting the residues of a protein essential to binding by analyzing protein-DNA interactions from an information theoretic perspective. Through the lens of mutual information, we explore which properties of protein sequence and structure are most useful in determining binding residues with a particular focus on sequence features. We find that the quantity of information carried in most features is small with respect to DNA-contacting residues, the bulk being provided by sequence features along with a select few structural features. Supplemental information for this article is available at http://www.cs.umn.edu/ -kauffman/supplements/psb2008.
authors.affiliation: Department of Computer Science, University of Minnesota, 117 Pleasant St. SE, Minneapolis, MN 55455, USA. kauffman@cs.umn.edu
authors.forename: Chris
authors.initials: C
authors.lastname: Kauffman
authors.forename: George
authors.initials: G
authors.lastname: Karypis
mesh_terms: D001665:Binding Sites; D019295:Computational Biology; D003198:Computer Simulation; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D030562:Databases, Protein; D007257:Information Theory; D008954:Models, Biological; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*
chemical_list: D011506:Proteins; D004247:DNA