Protein Engineering, Vol. 12, No. 3, 203-216,
March 1999
© 1999 Oxford University Press
Protein structural domain identification
Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
A simple method for the definition of protein structural domains is described that requires only 
-carbon coordinate data. The basic method, which encodes no specific aspects of protein structure, captures the essence of most domains but does not give high enough priority to the integrity of ß-sheet structure. This aspect was encouraged both by a bias toward attaining intact ß-sheets and also as an acceptance condition on the final result. The method has only one variable parameter, reflecting the granularity level of the domains, and an attempt was made to set this level automatically for each protein based on the best agreement attained between the domains predicted on the native structure and a set of smoothed coordinates. While not perfect, this feature allowed some tightly packed domains to be separated that would have remained undivided had the best fixed granularity level been used. The quality of the results was high and, when compared with a large collection of accepted domain definitions, only a few could be said to be clearly incorrect. The simplicity of the method allowed its easy extension to the simultaneous definition of domains across related structures in a way that does not involve loss of detail through averaging the structures. This was found to be a useful approach to reconciling differences among structural family members. The method is fast, taking less than 1 s per 100 residues for medium-sized proteins.
Keywords: Ising model/protein structure domains
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