Extraction of geometrically similar substructures: Least‐squares and Chebyshev fitting and the difference distance matrix

In analysis, comparison and classification of conformations of proteins, a common computational task involves extractions of similar substructures. Structural comparisons are usually based on either of two measures of similarity: the root‐mean‐square (r.m.s.) deviation upon optimal superposition, or the maximal element of the difference distance matrix. The analysis presented here clarifies the relationships between different measures of structural similarity, and can provide a basis for developing algorithms and software to extract all maximal common well‐fitting substructures from proteins.

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