Tamarind Bio illustrative settings and output interpretation

Reviewed 2026-09-30 using the live public catalog, REST contract, and tool documentation. These examples are **not authenticated validate-job results**. Replace file placeholders, read GET /tools/{name}/schema, then validate each settings object before a compute submission. Historical exact error messages are not a contract.

Authentication and discovery check

This read-only check does not submit jobs. Supply the user's deployment and key:

import os
import requests

base = os.environ.get("TAMARIND_BASE_URL", "https://app.tamarind.bio/api").rstrip("/")
headers = {"x-api-key": os.environ["TAMARIND_API_KEY"]}
response = requests.get(f"{base}/tools", headers=headers, timeout=(10, 60))
response.raise_for_status()
tools = response.json()
assert isinstance(tools, list)
print("[OK] Account tool catalog returned", len(tools), "entries")

To check a payload next, use /validate-job as shown in workflows. That call requires authentication even though it does not spend a compute job.

AlphaFold monomer and multimer

sequence is the public catalog's required setting for alphafold:

{"sequence": "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG"}

For a homodimer, this illustrative short sequence pair shows colon separation:

{"sequence": "MKTAYIAKQRQISFVKSHFSRQLEERLGLIE:MKTAYIAKQRQISFVKSHFSRQLEERLGLIE"}

It does not establish that these chains interact. Read optional model-count, recycle, MSA, and template fields from the account schema instead of assuming string versus numeric representations or defaults.

Boltz and Chai sequence modes

{"inputFormat": "sequence", "sequence": "MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEKAVQVKVKALP"}

The current public catalog makes inputFormat **optional with default "sequence"** for both tools. Boltz advertises sequence, list, molecules, and yaml; Chai advertises sequence, molecules, and list (no YAML mode in this catalog). Set a mode explicitly when useful, then supply its conditional fields. Do not claim that omitting inputFormat universally fails validation.

DiffDock with a SMILES ligand

{"proteinFile": "target.pdb", "ligandFormat": "SMILES",
 "ligandSmiles": "CC(=O)Oc1ccccc1C(=O)O"}

Upload an actual target first. The current proteinFile declaration accepts PDB and CIF extensions. ligandFormat defaults to "sdf/mol2 file"; set "SMILES" to activate ligandSmiles. The file branch uses ligandFile with SDF/MOL2.

AutoDock Vina with a SMILES ligand

{"receptorFile": "receptor.pdb", "ligandFormat": "smiles",
 "ligandSmiles": "CC(=O)Oc1ccccc1C(=O)O"}

This is the catalog-backed minimum branch, not a complete scientific docking protocol. Vina uses receptorFile, accepts PDB/CIF, and its ligandFormat values are lowercase "sdf"/"smiles" with default "sdf". Determine a meaningful search box from the receptor/pocket and read its current fields, units, and sampling settings from the full account schema. The public required-settings catalog does not verify optional box parameter names or their defaults; do not reuse coordinates from an unrelated target or claim arbitrary example coordinates are required API settings.

ProteinMPNN inverse folding

{"pdbFile": "backbone.pdb", "designedResidues": {"A": "1 2 3 4 5"}}

The selected residues must exist on chain A of the uploaded structure. The catalog currently declares PDB/CIF input and a space-separated residue-list representation. Its empty-map default does not justify assuming which chains or residues will be redesigned. Inspect the full schema to choose a model variant, sample count, and explicit design region, then validate. Fold generated sequences through the folding tool's sequence field, not a template parameter.

Outputs and failure interpretation

• Score is optional and can be JSON text, a number, or null; parse by actual type. Metrics and output filenames depend on the tool/task/version.
• /tools can expose outputs.mainCSV, task-specific outputs.byTask, column metadata, and filterMetrics. Use these and the actual archive to find data; do not assume every folder emits rank_*.pdb or every tool has pLDDT.
• pLDDT, pTM, and interface confidence are model confidence estimates, not proof of affinity, specificity, or experimental validation. Assess geometries and chemical validity and compare only compatible metrics/scales.
• Complete permits result retrieval but does not prove usable scientific output. Stopped/Failed require log inspection (fileName: "output.log").
• /result 202 means archive preparation: wait and repeat retrieval. It is not an instruction to run the scientific job again.
• /validate-job success returns the normalized settings to submit. An unknown key warning still needs correction; a typo in an optional field can otherwise run with the wrong default.
• Relative uploaded paths and JobName/path/to/file.ext references are distinct from inline content. Avoid inventing storage keys or treating arbitrary text as an existing file. Current documentation says redundant email prefixes are stripped; older double-prefix errors are no longer universal.