Real-to-bin conversion for protein residue distances

Abstract

Protein Structure Prediction (PSP) has achieved significant progress lately. Prediction of inter-residue distances by machine learning and their exploitation during the conformational search is largely among the critical factors behind the progress. Real values than bin probabilities could more naturally represent inter-residue distances, while the latter, via spline curves more naturally helps obtain differentiable objective functions than the former. Consequently, PSP methods that exploit predicted binned distances perform better than those that exploit predicted real-valued distances. To leverage the advantage of bin probabilities in getting differentiable objective functions, in this work, we propose techniques to convert real-valued distances into distance bin probabilities. Using standard benchmark proteins, we then show that our real-to-bin converted distances help PSP methods obtain three-dimensional structures with 4%-16% better root mean squared deviation (RMSD), template modeling score (TM-Score), and global distance test (GDT) values than existing similar PSP methods. Our proposed PSP method is named real to bin (R2B) inter-residue distance predictor, and its code is available from https://gitlab.com/mahnewton/r2b.

Keywords: Binned distance; Protein Structure Prediction; Real-valued distance; Residue-residue distance.