SwissTargetPrediction batch prediction — DeepSeek Harness plugin & agent skill

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Want to know which proteins a molecule — or a whole series — might act on? Hand it the SMILES. It submits each one to SwissTargetPrediction, waits for the prediction, and lays the results out as one table: target and common name, UniProt and ChEMBL ids, target class, probability, and the known actives behind each target (3D/2D). The same table is written to a CSV in the session workspace.

Note: This tool is unofficial and not affiliated with the Swiss Institute of Bioinformatics (SIB). Please respect their server usage policies. If the predictions go into research, cite Daina, Michielin & Zoete, Nucleic Acids Research 47(W1), W357–W364 (2019).

What you get

• A whole batch in one go. Paste one SMILES per line; submitting, waiting and collecting the results is the plugin's job.
• Everything the service reports, in one table. Target and common name, UniProt and ChEMBL ids, target class, probability, known actives (3D/2D).
• Salt forms handled for you. A hydrochloride, a sodium salt or another ionic form is desalted before submission — and neutralised where that is safe — with every change listed for you. SwissTargetPrediction takes one molecule per query, so pasting a salt as-is simply returns nothing.
• Three ways to run it. Ask the agent; type /swiss in the composer; or open the SwissTarget panel and paste your list.
• No blind waiting. Progress and elapsed time while it runs, results still there if you switch away, and a written reason for every molecule that failed.
• Human, mouse or rat.
• Results you can keep. The full table goes to a CSV in the session workspace, and the panel exports it on demand.
• English and Chinese UI.

Install

Into a Harness profile, straight from a release — nothing to clone:

dsh plugin --profile <profile> add https://github.com/YumeAyai/dsh-swiss-target/releases/latest/download/dsh-swiss-target.tar.gz

Or from the repository, or from a copy you already have:

dsh plugin --profile <profile> add github:YumeAyai/dsh-swiss-target
dsh plugin --profile <profile> add /absolute/path/to/this/directory

As an agent skill (the same directory is the skill bundle):

git clone https://github.com/YumeAyai/dsh-swiss-target.git ~/.dsh/skills/dsh-swiss-target

Usage

Ask the agent

swiss_target_batch(smiles=["CC(=O)OC1=CC=CC=C1C(=O)O", "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"])

| Parameter | Default | Meaning | |---|---|---| | smiles | — | One SMILES string per molecule, at most 25 per call | | organism | Homo_sapiens | Also Mus_musculus, Rattus_norvegicus | | output_csv | swiss_target_results.csv | Relative to the session workspace, or absolute |

From the composer

/swiss CC(=O)OC1=CC=CC=C1C(=O)O
/swiss {"smiles":["CCO","c1ccccc1"],"organism":"Homo_sapiens"}

One SMILES per line (# starts a comment), or the JSON payload the panel sends.

From the panel

Open a session, choose SwissTarget in the conversation view tabs, paste one SMILES per line, pick the organism and run. The results appear as a table, and Export CSV downloads them; the host also writes the whole batch into the workspace.

While it runs the panel shows progress and elapsed time — 5–60 seconds per molecule is normal. Switching tabs or sessions and coming back keeps the draft and the results.

Example output

| Target | Common name | Uniprot ID | ChEMBL ID | Target Class | Probability* | Known actives (3D/2D) | input_smiles | |---|---|---|---|---|---|---|---| | Cyclooxygenase-1 | PTGS1 | P23219 | CHEMBL221 | Oxidoreductase | 0.756 | 13 / 2 | CC(=O)OC1=CC=CC=C1C(=O)O |

Salt forms and mixtures

Most active pharmaceutical ingredients are weighed as a salt — a hydrochloride, a sodium salt, a tartrate — and SwissTargetPrediction takes one molecule per query: submitting [Cl-].CC(=O)Oc1ccccc1C(=O)O as-is returns nothing at all. So every line is converted before it is submitted:

| You submit | Actually submitted | What happened | |---|---|---| | [Cl-].CC(=O)Oc1ccccc1C(=O)O | CC(=O)Oc1ccccc1C(=O)O | chloride counter-ion dropped | | CN(C)CCOC(c1ccccc1)c1ccccc1.Cl | CN(C)CCOC(c1ccccc1)c1ccccc1 | neutral HCl adduct dropped | | CC(=O)[O-].[Na+] | CC(=O)O | sodium dropped, carboxylate neutralised | | [Na+].[O-]C(=O)c1ccccc1O | OC(=O)c1ccccc1O | sodium dropped, phenolate/carboxylate neutralised | | [NH3+]CC(=O)[O-] | NCC(=O)O | zwitterion neutralised | | C[N+](C)(C)CCOC(c1ccccc1)c1ccccc1.[Cl-] | quaternary parent | chloride dropped, the charge stays (no hydrogen to lose) | | CCO.c1ccccc1 | c1ccccc1 | a real mixture: largest fragment kept, the rest reported | | [Na+].[Cl-] | — | refused: counter-ions only |

Your structure is never rewritten beyond that: only counter-ions are dropped, and only charges that can be neutralised safely are touched — a nitro or a quaternary ammonium group is submitted as written. The original line and the submitted form each keep a CSV column (input_smiles, submitted_smiles), and every change is listed in the tool result and in the panel.

Good to know

• The service throttles. After a run of submissions it refuses new jobs for a while. The client retries each molecule three times, then marks that molecule as failed with its reason and finishes the rest. Retry the failed ones later.
• Caps. At most 25 molecules per call; at most the service's own top 100 targets per molecule.
• Timing. Submissions are sequential with a 2-second pause; one molecule usually takes 5–60 seconds.
• Organism. Human (default), mouse, rat.
• Predictions, not evidence. Do not present them as measurements.

License

This code is released under the ISC License. The data and predictions are owned by SwissTargetPrediction / SIB.

A Node.js port of the Python client swiss_target_batch, which keeps the original source and its own install instructions.