← API reference
Property prediction

AggreScan3D API

Map aggregation-prone patches onto a protein structure and score them.

Runs the AggreScan3D standalone package, which projects intrinsic aggregation propensities onto a structure and weights them by solvent exposure, giving a per-residue score and a total for the protein. The dynamic mode reruns the analysis over a CABS-flex ensemble instead of the single deposited conformation.

Web form Documentation ↗ Home page ↗ Source code ↗
Submit POST /api/aggrescan3d/

Queues a run and returns 202 with the job.

Schema GET /api/aggrescan3d/

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

Runtime

Installed by setup_system.sh into a Conda environment (the upstream package is Python 2.7-only); the mutate and auto_mutation modes additionally need a licensed FoldX install, and the dynamic mode needs CABS-flex, neither of which setup_system.sh installs · Python app (conda) · Expensive (min or hours)

License

Non-commercial. Free for academic use (Laboratory of Computational Biology, University of Warsaw). The mutate and auto_mutation modes call FoldX, which needs its own academic licence key; the dynamic mode calls CABS-flex, from the same lab. Commercial use of either requires a separate agreement.

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 aggrescan3d-demo Job name
pdb string file yes HEADER PASTE A PROTEIN PDB HERE Protein PDB file types .pdb,.ent.
chain string text no — Chain (optional) Restrict the analysis to one chain. Empty analyses the whole structure. up to 4 characters.
distance number number no 10.0 Aggregation sphere radius (angstroms) Residues within this radius of each alpha carbon contribute to its score. minimum 1, maximum 20, step 0.5.
dynamic boolean checkbox no false Score over a CABS-flex ensemble Much slower, but accounts for flexibility instead of scoring one conformation.
mutate string textarea no — Mutations to score (optional) One per line, as wild-type residue, mutant residue, position, and chain, for example MW1A. Needs FoldX.
auto_mutation number number no 0 Solubility mutations to suggest Ask A3D to propose this many stability-aware solubility mutations. 0 skips the search. Needs FoldX. minimum 0, maximum 10.
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/aggrescan3d/ \
  -H 'Content-Type: application/json' \
  -d '{
  "job_name": "aggrescan3d-demo",
  "pdb": "HEADER    PASTE A PROTEIN PDB HERE",
  "chain": "",
  "distance": 10.0,
  "dynamic": false,
  "mutate": "",
  "auto_mutation": 0
}'

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

statusMeaning
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

codeMeaning
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.