Correlated Mutations and Residue Contacts

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Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences (2019, background): “The unobserved variables that determine a protein’s ﬁtness, such as structure, function, and stability, leave a record in the distribution of observed natural sequences (Göbel et al., 1994).”
Protein sectors: evolutionary units of three-dimensional structure (2009, neutral): “…for the calculation of residue covariance, but often with the goal of identifying the pattern of contacts in the three dimensional structure (Gobel et al., 1994; Hamilton et al., 2004; Larson et al., 2000; Neher, 1994; Olmea and Valencia, 1997; Ortiz et al., 1999; Shindyalov et al., 1994;…”
Coevolution-based inference of amino acid interactions underlying protein function (2018, background): “The central premise is that the relevant energetic coupling of two residues in a protein should be reflected in the correlated evolution (coevolution) of those positions in sequences comprising a protein family (Göbel et al., 1994; Lockless and Ranganathan, 1999; Neher, 1994; Weigt et al., 2009).”