Open AccessProtein – DNA interactions: the story so far and a new method for prediction
Author(s) -
Jones Susan,
Thornton Janet M.
Publication year - 2003
Publication title -
comparative and functional genomics
Language(s) - English
Resource type - Journals
eISSN - 1532-6268
pISSN - 1531-6912
DOI - 10.1002/cfg.303
Subject(s) - template , protein data bank (rcsb pdb) , superposition principle , computational biology , structural motif , computer science , dna , motif (music) , protein structure , data mining , algorithm , biology , genetics , mathematics , biochemistry , physics , programming language , mathematical analysis , acoustics
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 DNA‐binding 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. Copyright © 2003 John Wiley & Sons, Ltd.