sugar chains

[zhulinyu0527-eng]

I would like to ask how to input sugar chains, such as BMA, MAN, NAG and so on.Thank you.

[rclune]

You can include sugar molecules the same way you would a ligand. For an example with RFD3 you can see the tutorial in PR #282, it will be added to the foundry documentation soon. For RF3, see the 7o1r_from_json example, it includes a NAG molecule.

If you are interested in designing backbones with RFD3 with sugars as part of the chain, RFD3na can do it for DNA/RNA chains, however it can't design backbones using general sugar molecules.

[clintonmholt]

Here's an example from a Rosettafold3 workshop!

Define 2 glycans commonly present on viral proteins

Glycan 1: biantennary complex — NAG-NAG-BMA-(MAN-NAG-GAL-SIA)₂

Asn ── NAG ── NAG ── BMA
                     ├── α1,3 ── MAN ── NAG ── GAL ── SIA
                     └── α1,6 ── MAN ── NAG ── GAL ── SIA

Glycan 2: high-mannose Man5 — NAG-NAG-BMA-(MAN)₃

Asn ── NAG ── NAG ── BMA
                     ├── α1,3 ── MAN ── MAN
                     └── α1,6 ── MAN

**These are included in the 2 json files attached which are the same other than which glycan is being modeled. Additionally I've included an MSA needed for accurate modeling. **

Run RF3 (both jobs run batched)

rf3 fold inputs='[sars2_rbd_complex_glyc.json, sars2_rbd_man5_glyc.json]' n_recycles=10 diffusion_batch_size=5 num_steps=50 out_dir="."

The files you need are attached below

sars2_rbd_complex_glyc.json
sars2_rbd_man5_glyc.json

sars2_rbd_wt.a3m.txt