TT3D: Leveraging precomputed protein 3D sequence models to predict protein-protein interactions

Samuel Sledzieski, Kapil Devkota, Rohit Singh, Lenore Cowen, Bonnie Berger

Abstract: High-quality computational structural models are now precomputed and available for nearly every protein in UniProt. However, the best way to leverage these models to predict which pairs of proteins interact in a high-throughput manner is not immediately clear. The recent Foldseek method of van Kempen et al. encodes the structural information of distances and angles along the protein backbone into a linear string of the same length as the protein string, using tokens from a 21-letter discretized structural alphabet (3Di).