Protein secondary structure analysis with a coarse-grained model

TL;DR

This paper introduces a geometrical model for analyzing protein secondary structures using only C-alpha atom positions, employing screw motions and polynomial interpolation to reliably identify structural elements.

Contribution

The study presents a novel coarse-grained model based solely on C-alpha atoms, offering an alternative to traditional methods like DSSP for secondary structure assignment.

Findings

The model accurately assigns secondary structures using C-alpha data.

Thresholds for screw parameters effectively distinguish structural elements.

Comparative analysis shows competitive performance with DSSP.

Abstract

The paper presents a geometrical model for protein secondary structure analysis which uses only the positions of the $C_{\alpha}$-atoms. We construct a space curve connecting these positions by piecewise polynomial interpolation and describe the folding of the protein backbone by a succession of screw motions linking the Frenet frames at consecutive $C_{\alpha}$-positions. Using the ASTRAL subset of the SCOPe data base of protein structures, we derive thresholds for the screw parameters of secondary structure elements and demonstrate that the latter can be reliably assigned on the basis of a $C_{\alpha}$-model. For this purpose we perform a comparative study with the widely used DSSP (Define Secondary Structure of Proteins) algorithm.