PMID:12169527

Citation	Steffen, NR, Murphy, SD, Tolleri, L, Hatfield, GW and Lathrop, RH (2002) DNA sequence and structure: direct and indirect recognition in protein-DNA binding. Bioinformatics 18 Suppl 1:S22-30
Abstract	Direct recognition, or direct readout, of DNA bases by a DNA-binding protein involves amino acids that interact directly with features specific to each base. Experimental evidence also shows that in many cases the protein achieves partial sequence specificity by indirect recognition, i.e., by recognizing structural properties of the DNA. (1) Could threading a DNA sequence onto a crystal structure of bound DNA help explain the indirect recognition component of sequence specificity? (2) Might the resulting pure-structure computational motif manifest itself in familiar sequence-based computational motifs?
Links	PubMed
Keywords	Algorithms; Amino Acid Sequence; Binding Sites; DNA, Bacterial/chemistry; DNA-Binding Proteins/chemistry; Escherichia coli Proteins/chemistry; Integration Host Factors/chemistry; Macromolecular Substances; Models, Chemical; Models, Molecular; Models, Statistical; Molecular Sequence Data; Protein Binding; Sequence Alignment/methods; Sequence Analysis, DNA/methods; Structure-Activity Relationship
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