Hotspots on target and scaffold protein for binder desing? #157
Cookiemaster33
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Hi there.
I really love the binder design function, especially coupling it with fold conditioning. I had some good results designing a protein that can bind to the hotspot regions on my target protein.
What I would love to do however, is to design binder proteins that are similar to an input structure, and at the same time bind the hotspot of my target just with a certain domain. Unfortunately, rfdiffusion spits out a lot of binders that bind the target with other domains. Thus, I need to do a lot of quality control and have to sift through structures to find "the needle in the haystack". (Does this make sense somehow?)
I have tried to play around with potentials, but it unfortunately went nowhere.
I think It would be fantastic if I could define hotspots, not only on my target protein, but also on the input pdbs that are used for conditioning. I know that rfdiffusion only uses secondary structure constrains to do the conditioning, so I understand that this might be a bit difficult to implement. But if there would be a solution for that in the future, I think that would be helpful to other people to (?). On the other hand, I maybe use the program wrong :D
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