Seeking script recommendations for minimized enzyme design using RFdiffusion2

[pengzichen1]

Hello
I am a newcomer to protein design and I have a question regarding RFdiffusion2. My goal is to design a minimized enzyme based on four conserved motifs and their corresponding catalytic site residues, which I have extracted from a native enzyme of interest.
Could you recommend some suitable shell scripts or workflows for accomplishing this task using RFdiffusion2? I would greatly appreciate any guidance, suggestions to relevant examples.

[roccomoretti]

At this point, I wouldn't recommend using RFdiffusion2 for new projects (just for recapitulating prior work). For new projects, I'd recommend switching to RFD3.

There are some enzyme design tutorials for RFD3, which should contain "walk-through" like steps which you should be able to adapt to your use case. In particular, there's an basic enzyme design tutorial, an intermediate enzyme design tutorial and a enzyme design examples page in the documentation. There's also an "Advanced Enzyme Design Tutorial" that's just been submitted as a PR ( RosettaCommons/foundry#379 ) -- there will be an associated video released with that last one, once it's ready to go.

[pengzichen1]

Thank you so much for your helpful advice!
I'll try it!