RFdiffusion3NA

Design protein, RNA and DNA with RFdiffusion3NA. Build chains of chosen lengths from scratch, or start from an input structure to scaffold a motif, design around a ligand or target, build a binder against chosen hotspots or perturb the structure by partial diffusion. Cyclic and dihedral symmetry are supported. Every design comes with chain-break, clash and radius-of-gyration metrics; the protein chains can then be redesigned with MPNN and checked by refolding.
8 designs
Estimated minimum cost: $—

Examples

Design specification

Starting point

Chains to design

One row per stretch of residues, up to 400 designed residues in total. Leave the longest length empty for a fixed length; a range lets each design pick its own. A change of polymer starts a new chain; tick the box to start one between two rows of the same polymer.

Contig: 40-50R

Symmetry and shape

Cyclic or dihedral assemblies of identical chains. Symmetric designs are sampled one at a time, which takes longer.

Biases protein designs toward fewer loops, mostly helices.

Sampling

Designs to generate, 1 to 50.

20 to 400; more steps cost more time. Designs × steps is at most 12000; designs run in batches of up to 8, so 50 count as 56.

Set it to reproduce a run; leave it empty for a random seed.