Many important principles underlying how protein molecular machines work lie beyond the pale of direct experimental observation. CHAIN (Contrast Hierarchical Alignment and Interaction Network ) analysis is a statistical solution to this problem that follows Mendel’s example: Just as Mendel inferred principles underlying genetic mechanisms from observed patterns of inherited traits, CHAIN analysis seeks to infer principles underlying molecular mechanisms from observed patterns in protein sequences—the cell’s own language for encoding those mechanisms.
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Trends Biochem Sci. 2007 Nov;32(11):487-93. Epub 2007 Oct 24.
The CHAIN program: forging evolutionary links to underlying mechanisms.