Toward a better understanding of structural divergences in proteins using different secondary structure assignment methods

Abstract

Structural disagreements on the location and quantity of secondary structure segments comprise a current challenging problem leading to several limitations for theoretical and applied research. This paper presents 116 structural evaluations by steric and hydrophobic interactions in secondary structures within a specific template group; determines simple prediction rules that calculate 88 occurrence frequencies of large and hydrophobic residues into target intra- and inter-subgroups with structure disagreements; and utilizes 42 comparisons between the methods PROMOTIF, DSSP and STRIDE. In the stereochemical predictions inside the subgroups there are predominantly excellent and/or good success amounts with their expected values, and the disclosure of a triple molecular mechanism by residue volumetric and hydrophobic ingredients. The method comparisons show high compatibility scores between them, therefore validating their seemingly incompatible assignments. Thus, the nonconsensual ascriptions are better understood and appreciated. Furthermore, such results suggest a broad utility of our assignment method for other benchmark datasets and known methods.