Grid-based prediction of torsion angle probabilities of protein backbone and its application to discrimination of protein intrinsic disorder regions and selection of model structures

Abstract

Background: Protein structure can be described by backbone torsion angles: rotational angles about the N-Cα bond (φ) and the Cα-C bond (ψ) or the angle between Cαi-1-Cαi-Cαi + 1 (θ) and the rotational angle about the Cαi-Cαi + 1 bond (τ). Thus, their accurate prediction is useful for structure prediction and model refinement. Early methods predicted torsion angles in a few discrete bins whereas most recent methods have focused on prediction of angles in real, continuous values. Real value prediction, however, is unable to provide the information on probabilities of predicted angles.

Results: Here, we propose to predict angles in fine grids of 5° by using deep learning neural networks. We found that this grid-based technique can yield 2–6% higher accuracy in predicting angles in the same 5° bin than existing prediction techniques compared. We further demonstrate the usefulness of predicted probabilities at given angle bins in discrimination of intrinsically disorder regions and in selection of protein models.

Conclusions: The proposed method may be useful for characterizing protein structure and disorder. The method is available at http://sparks-lab.org/server/SPIDER2/ as a part of SPIDER2 package.