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. 2016 May 12;25(7):1354–1362. doi: 10.1002/pro.2930

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© 2016 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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Predicted relative exchangeabilities (S) calculated from equilibrium amino acid frequencies and from a set of standard substitution matrices. The site‐specific amino acid frequencies were based on Pfam protein alignments and calculated with Eq. (5), whereas the substitution matrix exchangeabilities were calculated for Le and Gascuel15 (red), JTT13 (green), and Blossum6212 (purple). In all cases, the rate matrices from which the exchangeabilities were derived were normalized so that the average substitution rate was 1.0.