“AlphaFold3, unlike its predecessors, is capable of modelling proteins in concert with other molecules. But instead of releasing its underlying code — as was done with AlphaFold2 — DeepMind provided access through a web server that restricted the number and types of predictions scientists could make.

Crucially, the server prevented scientists from predicting how proteins would behave in the presence of potential drugs. But DeepMind’s decision to release the code changes that.

The company initially said that making AlphaFold3 available only through a web server struck the right balance between enabling access for research and protecting commercial interests. Isomorphic Labs, a DeepMind spin-off company in London, is applying AlphaFold3 to drug discovery.

But the publication of AlphaFold3 without its code or model weights — parameters obtained by training the software on protein structures and other data — drew criticism from scientists, who said that the move undermined reproducibility. DeepMind swiftly reversed course and said it would make an open-source version of the tool available within half a year.

Anyone can now download the AlphaFold3 software code and use it non-commercially. But for now, only scientists with an academic affiliation can access the training weights, and only on request.”‘

From Nature.