Structure prediction · Binder design

HighFold

Predict the structure of a cyclic peptide or a cyclic-peptide complex.

Runs HighFold, which folds cyclic peptides by feeding AlphaFold 2 a cyclic position offset matrix in place of its usual relative positional encoding, so head-to-tail and disulfide-bridged macrocycles are modelled as closed rather than as linear chains whose ends happen to meet.

Documentation ↗ Source code ↗

Input

Configure a small job

POST

Job name

Peptide sequence Join the chains of a complex with a colon; the first chain is the cyclic peptide.

Cyclic constraint Which constraints the cyclic offset matrix is built from.

Disulfide pairs (optional) Comma-separated 1-indexed cysteine pairs, for example 3-11,5-17. Inferred from the sequence when left empty.

MSA mode Short macrocycles have no useful alignment, so single-sequence is the usual choice.

Models

Recycles

Seeds per model

Random seed

Use PDB templates

Relax the top model with Amber Cleans up bond geometry at the cyclization point, at a few minutes of extra runtime.

Ready

Response

JSON result

{
  "status": "Ready for a request"
}