[the__alchemist]

Cool project! I have a question based on the video: What sort of work is it doing from the "Upload mmCIF file and specify number of molecules to generate" query? That seems like a broad ask. For example, it is performing ML inference on a data set of protein characteristics, or pockets in that protein? Using a ligand DB, or generating ligands? How long does that run take?

[denizkavi]

In this case the input to the model is the input structure of the protein target, i.e. you can define the whole search space for it to try to find a binder/drug against. We let you pick a preset recipe to follow at the top, which basically are common ways people are using this protocol for. The model itself can find a pocket, or the user can specify it if they know ahead of time. There is a very customizable variant for this tool, where you can set distances between individual atoms, make a custom scaffold for your starting molecule, but 90% of the time, the presets tend to be sufficient.

Runs vary significantly between models/protocols used, some generative models can take several hours, while some will run a few seconds. We have tools that would screen against DBs if the goal is to find an existing molecule to act against the target, but often, people will import and existing starting point and modify it or design completely novel ones on the platform.