Carbonic Anhydrase (5yui) active site modelling

[ArnoldAndersson123]

Hi,

I want to model Carbonic Anhydrase (5yui) active site, an enzyme included in table 9 in Supplementary Methods article, and have below settings.

Are there any additional settings I should include or change any existing?

---

inference.output_prefix=outputs/carbonicanhydrase_4_script
inference.num_designs=4
inference.input_pdb=/content/RFdiffusion/examples/input_pdbs/5yui.pdb
'contigmap.contigs=[5-30/A93-97/5-20/A118-120/10-35/A198-200/10-30]'
inference.ckpt_override_path=/content/RFdiffusion/models/ActiveSite_ckpt.pt

BR, Arnold

[joewatchwell]

This looks good to me! If you have a substrate in there, you could use the substrate contact potential - there's an example in the 'design_enzyme' example script!

[ArnoldAndersson123]

Hi and thanks for the comment!

I have looked at the example file but in this case the substrates are small (CO2 and H2O) and the reaction is catalyzed by an Zn ion, so the reactive pocket is simple. I have made some 50 design and picked the most promising to move on to express and check for activity in the lab.

One more thing I wanted to ask about is tips on what to think of if I want to make a "superstructure" like an icosahedral containing multiple copies of the novel design above. Do you have any tips what I should think of if I want a self assembling structure?

BR, Arnold