Structure prediction · Binder design

HighFold

(Work in Progress)

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 ↗ Paper ↗ Source code ↗ License ↗

No jobs before this; it will run immediately.

Not logged in. Register an account to keep track of your jobs and results, and add presets and bookmarks. Email results to this address when complete:

Ready

Job name

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

Disulfide bridges (optional) Comma-separated 1-indexed residue pairs in the cyclic chain, for example 3-11,5-17. HighFold always closes the backbone head-to-tail; these add disulfide bridges on top of it.

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

Endpoint POST /api/highfold/

Send JSON or standard form data. A GET request returns this tool's field schema.

API reference for HighFold →