Transferrable End-to-End Learning for Protein Interface Prediction

Raphael J. L. Townshend, Rishi Bedi, Ron O. Dror

Abstract: While there has been an explosion in the number of experimentally determined, atomically detailed structures of proteins, how to represent these structures in a machine learning context remains an open research question. In this work we demonstrate that representations learned from raw atomic coordinates can outperform hand-engineered structural features while displaying a much higher degree of transferrability. To do so, we focus on a central problem in biology: predicting how proteins interact with one another—that is, which surfaces of one protein bind to which surfaces of another protein. We present Siamese Atomic Surfacelet Network (SASNet), the first end-to-end learning method for protein interface prediction. Despite using only spatial coordinates and identities of atoms as inputs, SASNet outperforms state-of-the-art methods that rely on hand-engineered, high-level features. These results are particularly striking because we train the method entirely on a significantly biased data set that does not account for the fact that proteins deform when binding to one another. Demonstrating the first successful application of transfer learning to atomic-level data, our network maintains high performance, without retraining, when tested on real cases in which proteins do deform.

Keywords: transfer learning, protein interface prediction, deep learning, structural biology

TL;DR: We demonstrate the first successful application of transfer learning to atomic-level data in order to build a state-of-the-art end-to-end learning model for the protein interface prediction problem.