Structure prediction · Binder design

HighFold API

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.

Web form Documentation ↗ Source code ↗

Submit POST /api/highfold/

Queues a run and returns 202 with the job.

Schema GET /api/highfold/

Returns this tool's metadata and the fields below, as JSON.

Request body

Fields

The same names the web form posts. See the field type table for what each kind means over HTTP.

Name	Type	Required	Default	Description
`job_name`	string text	no	`highfold-demo`	Job name
`peptide_sequence`	string textarea	yes	`GNLWATGHFMGGSGSGSG`	Peptide sequence Join the chains of a complex with a colon; the first chain is the cyclic peptide.
`cyclic_constraint`	string select	no	`head_to_tail`	Cyclic constraint Which constraints the cyclic offset matrix is built from. One of: `head_to_tail`, `disulfide`, `both`, `none`.
`disulfide_pairs`	string text	no	`—`	Disulfide pairs (optional) Comma-separated 1-indexed cysteine pairs, for example 3-11,5-17. Inferred from the sequence when left empty.
`msa_mode`	string select	no	`single_sequence`	MSA mode Short macrocycles have no useful alignment, so single-sequence is the usual choice. One of: `single_sequence`, `mmseqs2_uniref_env`, `mmseqs2_uniref`.
`num_models`	number number	no	`5`	Models minimum 1, maximum 5.
`num_recycles`	number number	no	`3`	Recycles minimum 0, maximum 48.
`num_seeds`	number number	no	`1`	Seeds per model minimum 1, maximum 16.
`seed`	number number	no	`0`	Random seed minimum 0, maximum 2147483647.
`use_templates`	boolean checkbox	no	`false`	Use PDB templates
`amber_relax`	boolean checkbox	no	`false`	Relax the top model with Amber Cleans up bond geometry at the cyclization point, at a few minutes of extra runtime.

Example

A request that runs

These are the defaults, exactly as the web form would post them.

curl -X POST https://www.athanortools.com/api/highfold/ \
  -H 'Content-Type: application/json' \
  -d '{
  "job_name": "highfold-demo",
  "peptide_sequence": "GNLWATGHFMGGSGSGSG",
  "cyclic_constraint": "head_to_tail",
  "disulfide_pairs": "",
  "msa_mode": "single_sequence",
  "num_models": 5,
  "num_recycles": 3,
  "num_seeds": 1,
  "seed": 0,
  "use_templates": false,
  "amber_relax": false
}'

The reply is 202 with a queued job; poll its status_url until status is succeeded or failed. See the quick start for the whole exchange.

Responses

What comes back

status	Meaning
`queued`	Accepted, waiting for the jobs ahead of it. `position` counts how many those are.
`running`	The tool is executing now.
`succeeded`	Finished; `result` holds the tool's output and `license` the terms it came under.
`failed`	Finished; `error` holds a code and a message.

Errors

code	Meaning
`invalid_input`	The client supplied invalid or incomplete input.
`tool_unavailable`	The requested third-party dependency is not available on this host.
`execution_failed`	A configured third-party process exited unsuccessfully.
`internal_error`	An adapter failed in a way it does not describe. The detail is in the server log, not the response.
`not_found`	No job has that id. Finished jobs are dropped eventually.