Computational methods to predict protein-protein interaction (PPI) typically segregate into sequence-based "bottom-up" methods that infer properties from the characteristics of the individual protein sequences, or global "top-down" methods that infer properties from the pattern of already known PPIs in the species of interest. However, a way to incorporate top-down insights into sequence-based bottom-up PPI prediction methods has been elusive. We thus introduce Topsy-Turvy, a method that newly synthesizes both views in a sequence-based, multi-scale, deep-learning model for PPI prediction. While Topsy-Turvy makes predictions using only sequence data, during the training phase it takes a transfer-learning approach by incorporating patterns from both global and molecular-level views of protein interaction. In a cross-species context, we show it achieves state-of-the-art performance, offering the ability to perform genome-scale, interpretable PPI prediction for non-model organisms with no existing experimental PPI data. In species with available experimental PPI data, we further present a Topsy-Turvy hybrid (TT-Hybrid) model which integrates Topsy-Turvy with a purely network-based model for link prediction that provides information about species-specific network rewiring. TT-Hybrid makes accurate predictions for both well- and sparsely-characterized proteins, outperforming both its constituent components as well as other state-of-the-art PPI prediction methods. Furthermore, running Topsy-Turvy and TT-Hybrid screens is feasible for whole genomes, and thus these methods scale to settings where other methods (e.g., AlphaFold-Multimer) might be infeasible. The generalizability, accuracy and genome-level scalability of Topsy-Turvy and TT-Hybrid unlocks a more comprehensive map of protein interaction and organization in both model and non-model organisms.

Topsy-Turvy and TT-Hybrid are described in the paper "Predicting the missing link: synthesizing protein network and sequence information with Topsy-Turvy" by Rohit Singh, Kapil Devkota, Sam Sledzieski, Bonnie Berger, and Lenore Cowen.

Topsy-Turvy leverages bottom-up predictions from D-SCRIPT and top-down predictions from GLIDE.

Topsy-Turvy is now available as part of the D-SCRIPT package (run with --topsyturvy):
pip install dscript