Atlas of protein sequence and structure

By M. A. Chang, M. O. Dayhoff, R. Eck, M. R. Sochard. 1965

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Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution. (1997, methodology): “The other three methods are all correlations of the model was used ( Dayhoff et al., 1978 ), but any other MDM change between residues in sequence pairs: model could be easily substituted.”
A method to identify protein sequences that fold into a known three-dimensional structure. (1991, methodology): “In short, the table of 3D-ID scores provides the link of 3D structure to ID sequence in the 3D structure profile method in the same way that the Dayhoff mutational matrix (27, 35) supplies the link between two sequences in the earlier sequence profile method (25).”
Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. (2000, methodology): “For example, in the case of maximum-parsimony (MP) methods (Eck and Dayhoff 1966; Fitch 1971), the minimum number of evolutionary changes that explains the entire sequence evolution (tree length [TL]) is computed for each topology, and the topology showing the smallest TL value is chosen as the…”