RosettaCommons / RosettaCommons/RFdiffusion
Design small molecule binding proteins [potentials.guiding_potentials]
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Description
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
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Research direction
Start with Extended Data Fig. 6 and Methods 4.4, then use the provided potentials.guiding_potentials example as the scope for the explanation. Document what potentials.guide_scale, substrate_contacts, s, r_0, rep_r_0, rep_s, and rep_r_min mean in this command, including how potentials.substrate=LLK relates to them. Done means a newcomer can understand and use the example without needing an additional clarification.
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Assessment
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- documentation
- Issue type
- Documentation
- Difficulty
- 3/5
- Estimated time
- 1-2 days
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- Stale
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- Newbie friendliness
- 30/100