PROSS: Dihedral Angle-Based Secondary Structure Assignment

Introduction

Several methods have been developed for assigning a protein's secondary structure from information in a PDB file (i.e. x,y,z-coordinates). All methods use some combination of hydrogen-bonding patterns, backbone dihedral angles and idealized templates of α-helices, β-turns and β-strands. PROSS is one such method. In PROSS, secondary structure assignments are based solely on the backbone dihedral angles.

You may download a Python program to calculate secondary structure or use the web server.

Method

1. Compute the φ and ψ values for each residue of the protein and assign a letter code based on either the figure shown below on the left (Course grained grid) or on the right (Fine grain grid).



For example a residue with φ = -64° and ψ = -43° will be assigned a letter code of 'O' in he course grained grid and a letter code of 'Ee' in the fine grained grid.

2. Individual residues are classified into different secondary structures according to the following definitions for the course grained or fine grained grids.