%0 Journal Article
%T Protein¨CDNA Interactions: The Story so Far and a New Method for Prediction
%A Susan Jones
%A Janet M. Thornton
%J Comparative and Functional Genomics
%D 2003
%I Hindawi Publishing Corporation
%R 10.1002/cfg.303
%X This review describes methods for the prediction of DNA binding function, and specifically summarizes a new method using 3D structural templates. The new method features the HTH motif that is found in approximately one-third of DNAbinding protein families. A library of 3D structural templates of HTH motifs was derived from proteins in the PDB. Templates were scanned against complete protein structures and the optimal superposition of a template on a structure calculated. Significance thresholds in terms of a minimum root mean squared deviation (rmsd) of an optimal superposition, and a minimum motif accessible surface area (ASA), have been calculated. In this way, it is possible to scan the template library against proteins of unknown function to make predictions about DNA-binding functionality.
%U http://www.hindawi.com/journals/cfg/2003/568038/abs/