Aller directement au contenu principal

Rédiger un PREreview

Have protein-ligand cofolding methods moved beyond memorisation?

Publié
Serveur de preprints
bioRxiv
DOI
10.1101/2025.02.03.636309

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.

Vous pouvez rédiger un PREreview de Have protein-ligand cofolding methods moved beyond memorisation?. Un PREreview est une évaluation d'un preprint et peut varier de quelques phrases à un rapport détaillé, semblable à un rapport d'évaluation par les pairs organisé par une revue.

Avant de commencer

Nous vous demanderons de vous connecter avec votre identifiant ORCID iD. Si vous n'en avez pas, vous pouvez en créer un.

Qu’est-ce qu’un ORCID iD ?

Un ORCID iD est un identifiant unique qui vous distingue de toute personne ayant le même nom ou nom similaire.

Commencer maintenant