He said that for the interactions of proteins with small (drug-like) molecules AlphaFold 3 showed 76% accuracy in a benchmark test (versus 52% for the next best tool).
Right. The benchmark (their test set) just compares 3D structures.
Side note: 52% also seems low for Vina, but I haven’t looked into this further. Maybe the benchmark is hard, or maybe the “search space” (user-specified) was too big.
On their other test (in their Extended Data), both Vina and AF3 do much better.
Unlike Vina, AF3 only predicts 3D structures, I believe. It does not predict binding affinities.
AlphaFold 2 was only predicting 3D structures. From the abstract of the Alpha Fold 3 paper:
The FastCompany article says:
Right. The benchmark (their test set) just compares 3D structures.
Side note: 52% also seems low for Vina, but I haven’t looked into this further. Maybe the benchmark is hard, or maybe the “search space” (user-specified) was too big.
On their other test (in their Extended Data), both Vina and AF3 do much better.