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AlphaFold 3 predicts protein structures with remarkable accuracy, yet how structural information emerges within the model remains poorly understood. Here, through causal interventions on internal representations and direct probing of every Pairformer block, we trace the formation of global protein geometry and identify...
Metabolites are generally viewed as substrates, products, cofactors, or regulators of individual proteins, whereas metabolites recurring across many protein families are often regarded as promiscuous binders. Here, we analyzed 989,058 BioLiP2 protein–ligand binding sites and assigned 929,546 sites to ECOD v295 homologo...
A global metabolite-mediated architecture with the capacity to coordinate proteins across otherwise distinct cellular systems is revealed and experimentally established metabolite-dependent complexes validate the local mechanism independently of LIGMAP.
Addressing and predicting ligand-binding sites in protein structures, as well as the prediction of reliable structures of proteins interacting with other proteins, will be pivotal for fully details of structural mechanisms and dynamics.
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