drug-discovery-prompts/upstream/K-Dense-AI-scientific-agent-skills/skills/tamarind/references/tool_catalog.md

title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated

title	task	lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	author	validated
Tamarind Bio tool catalog		import	https://github.com/K-Dense-AI/scientific-agent-skills/blob/0807ddbc/skills/tamarind/references/tool_catalog.md	0807ddbc	2026-06-30	prompt	accepted	upstream	false

Tamarind Bio tool catalog

Tamarind exposes hundreds of tools through one uniform job API. The catalog changes frequently — always enumerate at runtime with GET /tools (or MCP getAvailableTools) rather than hardcoding names. This file is a map for interpreting what you get back.

How to discover

REST GET /tools returns the full list (it does not filter server-side). Filter client-side:

tools = requests.get(f"{BASE}/tools", headers=HEADERS).json()      # a list
docking = [t for t in tools if "vina" in t["name"].lower()]

Each REST tool entry carries: name (the type you submit), displayName, description, github, paper, and settings (the inline parameter schema). REST entries do not include categories/tags.

MCP getAvailableTools(search=..., modality=..., function=...) filters server-side and returns entries with categories and tags (category/tag are deprecated aliases of modality/function, still honored).

Modalities and functions (the two filter axes)

Don't hardcode the filter vocabulary — it drifts as tools are added. Fetch it live: listModalities() returns the molecule-type axis (protein, antibody, enzyme, peptide, nucleic-acid, small-molecule, small-molecule-binding-protein, cryoem, …); listTags() returns the function axis (structure-prediction, protein-design, binder-design, protein-ligand-docking, binding-affinity, inverse-folding, developability, molecular-dynamics, finetuning, …). Each entry carries value, label, description, and a live toolCount. Every getAvailableTools response also includes availableCategories / availableTags arrays computed from the current catalog. Filter with getAvailableTools(modality=..., function=...).

Representative tool families

Verify exact names and availability with /tools — these are common anchors, not an exhaustive or guaranteed list.

Structure prediction / folding

• alphafold — AlphaFold; monomer + multimer, MSA + templates, recycles, relaxation.
• boltz — Boltz-2; structure + affinity, biomolecular complexes incl. ligands.
• chai — Chai-1; complex structure prediction with optional MSA.
• esmfold / esmfold2 — fast single-sequence folding.

Protein / binder design

• rfdiffusion — protein/binder design and motif scaffolding.
• boltzgen — generative design.
• bindcraft — binder design.
• proteinmpnn / ligandmpnn — inverse folding (sequence given backbone; ligand-aware variant).

Docking / affinity

• boltz / chai — co-fold the ligand into the complex (predict the bound structure); the default for protein-small-molecule docking.
• autodock-vina — classical docking into a known pocket; the pick for fast, large-scale screening.
• Boltz/affinity tools — binding-affinity prediction.

Antibody

• Antibody language models and generators, humanization, developability, immunogenicity scoring.

MSA / utilities

• MSA generation tools feed downstream folding; utilities cover format conversion, scoring, and analysis.

Reading a tool schema

getJobSchema(jobType) (MCP) or the /tools entry returns a parameters list. Each parameter has:

• name, type (sequence, number, boolean, dropdown, file types like pdb/cif/sdf, …)
• descr, displayName
• required, default
• options / optionsDescr (for dropdowns), lowerBound / upperBound / lengthLimit
• conditionals — applies only when another field has a given value
• exclude (["api"] / ["batch"]) — omit on that surface
• list: true — accepts multiple values/files
• example — a sample value

(Org-gated parameters are filtered server-side: getJobSchema drops a param your account isn't authorized for and never returns the old restrictOrgs key.)

Top-level tool metadata also includes a hint, and getJobSchema returns an exampleJob built from each parameter's example/default — start from that (then validateJob it) rather than hand-building settings.

Always read the schema before constructing settings, and run validateJob to confirm before submitJob.