Protein Contact Map Refinement for Improving Structure Prediction Using Generative Adversarial Networks

Bioinformatics. 2021 Mar 31;37(19):3168-3174. doi: 10.1093/bioinformatics/btab220. Online ahead of print.

Abstract

Motivation: Protein structure prediction remains as one of the most important problems in computational biology and biophysics. In the past few years, protein residue-residue contact prediction has undergone substantial improvement, which has made it a critical driving force for successful protein structure prediction. Boosting the accuracy of contact predictions has, therefore, become the forefront of protein structure prediction.

Results: We show a novel contact map refinement method, ContactGAN, which uses Generative Adversarial Networks (GAN). ContactGAN was able to make a significant improvement over predictions made by recent contact prediction methods when tested on three datasets including protein structure modeling targets in CASP13 and CASP14. We show improvement of precision in contact prediction, which translated into improvement in the accuracy of protein tertiary structure models. On the other hand, observed improvement over trRosetta was relatively small, reasons for which are discussed. ContactGAN will be a valuable addition in the structure prediction pipeline to achieve an extra gain in contact prediction accuracy.

Availability: https://github.com/kiharalab/ContactGAN.

Supplementary information: Supplementary data are available at Bioinformatics online.