Amino Acid Clustering

In molecular biology a fundamental problem is that of relating functional effects to structural features of the arrangement of amino acids in protein chains. Clearly, there are some features that have localized deterministic origin from the geometrical organization of the helices; other features seem to be of a more stochastic character with a degree of stability persisting over long sequences that approximates to stationarity. These latter features were the subject of our recent study [34], which we outline in this chapter. We make use of gamma distributions to model the spacings between occurrences of each amino acid; this is an approximation because the molecular process is of course discrete. However, the long protein chains and the large amount of data lead us to believe that the approximation is justified, particularly in light of the clear qualitative features of our results.