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Many longer polypeptide chains appear to fold into more than one distinct unit, or domain. Domains can only be defined subjectively, but they are usually unambiguously distinguishable by eye as self-contained units of structure, and have distinct hydrophobic cores. The automatic definition of domains[Swindells, 1995b,Islam et al., 1995,Siddiqui & Barton, 1995] is currently unreliable, despite the obvious need for such methods as the number of determined protein structures continues to grow.