RosettaCommons
Design small molecule binding proteins [potentials.guiding_potentials]
Your work is excellent, and I want to design small molecule binding proteins with your moldes. But I'm afraid I can't understand the meaning of these parameters, after consulting Extended Data Fig. 6 and Methods 4.4. Can you explain this part in detail? Thank you very much for your reply.
# We specify the identity of the substrate molecule (from which to apply the potential)
potentials.guide_scale=1 'potentials.guiding_potentials=["type:substrate_contacts,s:1,r_0:8,rep_r_0:5.0,rep_s:2,rep_r_min:1"]' potentials.substrate=LLK
Run in the same problem. Trying to understand whether the substrate identity is taken from the pdb input, or the potential should be specified somehow differently? Looked into the documentation, but this "potentials.substrate=LLK" is mentioned only in the design_enzyme.sh. @Lyueyang2020, any advance so far?
The somewhat described part regarding potentials can be found in README.md, line 398 ### Using Auxiliary Potentials .
Also, an extensive guide is available at https://huggingface.co/blog/AmelieSchreiber/rfdiffusion-potentials
Regarding the ligand:
Run in the same problem. Trying to understand whether the substrate identity is taken from the pdb input, or the potential should be specified somehow differently? Looked into the documentation, but this "potentials.substrate=LLK" is mentioned only in the design_enzyme.sh. @Lyueyang2020, any advance so far?"
The ligand is indeed taken from the input PDB. In the model example, input structure 5an7 contains a ligand "LLK".