A multivariate analysis method for discriminating protein secondary structural segments

Using discriminant analysis, three types of protein secondarystructure segments—helices, ß-strands and coils—arediscriminated by amino acid sequence information alone. A variablein the discriminant analysis is defined by the amino acid indexused to represent the sequence data and by the calculation methodused to extract a feature in this representation. Thus, thethree types of secondary structure segments derived from a setof non-homologous proteins from the Protein Data Bank are analyzedby 888 variables, which correspond to the mean, standard deviation,3.6-residue periodicity and 2-residue periodicity for the numericalprofiles determined from 222 published amino acid indices. Thesevariables are combined to obtain best discrimination of thethree types of segments. When up to three variables are combined,the best discrimination rate was 75%. The variables selectedconsist of the mean of propensity (or turn propensity), themean of ß propensity, and the 3.6-residue periodicityof hydrophobicity. This variable selection procedure can alsobe applied to other types of discrimination problem, once groupsof sequence data are properly organized.