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baker-laboratory / RoseTTAFold-All-Atom

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protein small molecule binding prediction algorithm #88

Open simonkim1347 opened 2 months ago

simonkim1347 commented 2 months ago

when multiple small molecule inputs (B, C, D...) predicted with one protein molecule result clashes between small molecules. I assume that they don't consider interactions between small molecules... is there any plan to modify this algorithm?

r-krishna commented 2 months ago

We have observed that this happens when there are many molecules and the network is unsure on where to place them. We are working on improving the network accuracy in these cases

amelie-iska commented 1 month ago

I could see both kinds of output being useful, one where you just want to know which small molecules hit the target, and the other to know how they compete with one another for that target.