ConTemplate: exploiting the protein databank to propose ensemble of conformations of a query protein of known structure
© Narunsky and Ben-Tal; licensee BioMed Central Ltd. 2014
Published: 11 February 2014
We demonstrate the method with the kinase domain of the Epidermal Growth Factor Receptor (EGFR). Using the inactive conformation as our query, we reproduce the active conformation  with root mean square deviation (RMSD) of 1.76Å, based on the query's structural similarity to the inactive conformation of Abl tyrosine-kinase , together with the known active conformation of the latter kinase . The sequence identity between the two kinase domains is only 40%, and the fact that they share similar active and inactive conformations might not be obvious.
The idea of inferring new conformations of a protein of interest based on known conformations in related proteins is not new. However, to the best of our knowledge, ConTemplate is the first automated implementation of this approach.
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