Have protein-ligand co-folding methods moved beyond memorisation?

Abstract

Deep learning has driven major breakthroughs in protein structure prediction, however the next critical advance is accurately predicting how proteins interact with small molecule ligands, to enable real-world applications such as drug discovery. Recent cofolding methods aim to address this challenge, but evaluating their performance has been inconclusive due to the lack of relevant bench-marking datasets. Here we present a comprehensive evaluation of four leading all-atom cofolding methods using our newly introduced benchmark dataset Runs N Poses, which comprises 2,600 high-resolution protein-ligand systems released after the training cutoff used by these methods. We demonstrate that current cofolding approaches largely memorise ligand poses from their training data, hindering their use for de novo drug design. With this assessment and benchmark dataset, we aim to accelerate progress in the field by allowing for a more realistic assessment of the current state-of-the-art deep learning methods for predicting protein-ligand interactions.