<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>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.</p>
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Comp Funct Genomics. 2003 Jul; 4(4):428-431