期刊
COMPARATIVE AND FUNCTIONAL GENOMICS
卷 4, 期 4, 页码 428-431出版社
HINDAWI LTD
DOI: 10.1002/cfg.303
关键词
DNA-binding; helix-turn-helix; motif; structural template
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 (C) 2003 John Wiley Sons, Ltd.
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