Historical Criteria for Structural Classes of Proteins in Percentages: After 20 Years

Abstract

Two decades ago scientists proposed some criteria for the structural classes in percentages. Today experts at SCOP classified hundreds of thousands of proteins into one of the four structural classes manually by inspection, and observation. Nakashima et al. gave a classification criteria. P.Y. Chou also proposed another method to classify proteins according their residue contents in three conformations, helix, sheet, and coil. Later P.Y. Chou revised his method. Today SCOP listed around 100.000 proteins with their structural classes. In this paper two datasets will be used to reveal the percentages of residues in α-Helices, β-sheets, and coils in proteins of classes all α, all β, α+β, and α/β, in the classifications made by experts in SCOP. The first of the data bases is PDBselect25 which contains 1670 twilight zone proteins whose similarity is less than 25%. The second data base BF30 consists of 10294 proteins picked from PDB database with the similarity threshold of 30%. Structural classes of these proteins are taken from SCOP database. It is seen that there is a very poor correlation between historical criteria, and SCOP’s scientists’ intuition in classification of proteins into structural classes.