Protein structural domain identification

A simple method for the definition of protein structural domainsis described that requires only -carbon coordinate data. Thebasic method, which encodes no specific aspects of protein structure,captures the essence of most domains but does not give highenough priority to the integrity of ß-sheet structure.This aspect was encouraged both by a bias toward attaining intactß-sheets and also as an acceptance condition on the finalresult. The method has only one variable parameter, reflectingthe granularity level of the domains, and an attempt was madeto set this level automatically for each protein based on thebest agreement attained between the domains predicted on thenative structure and a set of smoothed coordinates. While notperfect, this feature allowed some tightly packed domains tobe separated that would have remained undivided had the bestfixed granularity level been used. The quality of the resultswas high and, when compared with a large collection of accepteddomain definitions, only a few could be said to be clearly incorrect.The simplicity of the method allowed its easy extension to thesimultaneous definition of domains across related structuresin a way that does not involve loss of detail through averagingthe structures. This was found to be a useful approach to reconcilingdifferences among structural family members. The method is fast,taking less than 1 s per 100 residues for medium-sized proteins.