Antibody design · Binder design · Protein Design

mBER API

Design VHH (nanobody) binders against a target by backprop through AlphaFold-Multimer.

Runs mBER (Manifold Binder Engineering and Refinement) through its mber-vhh command-line tool, which designs VHH binders with the ColabDesign backpropagation loop against a target structure, optionally steered onto named hotspots, and keeps every trajectory that clears its iPTM and pLDDT filters. scFv design is not exposed by this CLI in the open-source release.

Web form Documentation ↗ Source code ↗

Submit POST /api/mber/

Queues a run and returns 202 with the job.

Schema GET /api/mber/

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	`mber-demo`	Job name
`target_pdb`	string file	yes	`HEADER PASTE A TARGET ANTIGEN PDB HERE`	Target antigen PDB file types .pdb,.ent,.cif.
`target_chains`	string text	yes	`A`	Target chains Comma-separated if the target is bound across more than one chain, for example A,B. up to 20 characters.
`hotspots`	string text	no	`A56`	Epitope hotspots (optional) Comma-separated target residues, for example A56,A57. Empty lets mBER bind anywhere on the target.
`num_accepted`	number number	no	`10`	Designs to keep The run stops once this many trajectories have passed the iPTM/pLDDT filters. minimum 1, maximum 1000.
`max_trajectories`	number number	no	`1000`	Trajectories to attempt Upper bound on attempts if num_accepted is never reached. minimum 1, maximum 100000.
`min_iptm`	number number	no	`0.75`	Minimum iPTM minimum 0, maximum 1, step 0.05.
`min_plddt`	number number	no	`0.7`	Minimum pLDDT minimum 0, maximum 1, step 0.05.

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/mber/ \
  -H 'Content-Type: application/json' \
  -d '{
  "job_name": "mber-demo",
  "target_pdb": "HEADER    PASTE A TARGET ANTIGEN PDB HERE",
  "target_chains": "A",
  "hotspots": "A56",
  "num_accepted": 10,
  "max_trajectories": 1000,
  "min_iptm": 0.75,
  "min_plddt": 0.7
}'

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.