Documentation

Overview

TargetGen designs new drug-like molecules for a protein you choose. You give it a 3D structure, pick the binding site, and it generates molecules shaped to fit that site. You can then filter them by drug-likeness and download them.

1. STEP 1
   Load a protein
   A PDB ID or your own file
2. STEP 2
   Pick the site
   A detected pocket, a ligand, or coordinates
3. STEP 3
   Generate
   New molecules built inside the site
4. STEP 4
   Filter and download
   SDF, MOL2 or CSV

Quick start

1. 1Go to the home page and sign in with Google. Loading a structure needs an account.
2. 2Type a 4-character PDB ID such as 3POZ and press Fetch, or upload your own .pdb or .ent file (up to 25 MB).
3. 3On the target page, TargetGen detects binding pockets automatically. Choose the one you want, or pick a ligand already in the structure, or enter coordinates by hand.
4. 4Set drug-likeness constraints on the next page, or keep the defaults.
5. 5On the generate page choose how many molecules you want and click Generate molecules. Confirm the popup to start. The run uses one credit per molecule.
6. 6Watch the progress, or close the tab. You can leave the page and come back, and you can ask to be emailed when it finishes.
7. 7Open the results, filter and sort them, view them in 3D, and download them.

Choosing a binding site

The site tells the model where in the protein to build molecules. There are three ways to set it.

Pocket detection takes around 15 seconds. The 3D viewer highlights the selected site so you can check it before spending credits.

Generation settings

How long it takes. Roughly 15 seconds per molecule, so 20 molecules take about 5 minutes. If other runs are ahead of yours you wait in a queue first, and the page shows your position.

You may get fewer molecules than you asked for. Some generated molecules can't be turned into a valid structure and are discarded. The cost is based on the number you request.

Reading your results

Each molecule comes with properties calculated from its structure:

Use the constraint filters to keep molecules within ranges you care about, such as MW, LogP, HBD, HBA, TPSA, QED and rotatable bonds, and to exclude substructures. Sort by QED, MW, LogP, TPSA, HBA or HBD. Open any molecule to see it posed in the binding site in 3D.

Downloads. Get the molecules as SDF (3D structures),MOL2 or CSV (SMILES and properties). The download respects your current filters.

Credits, plans and limits

One credit pays for one requested molecule. Credits come from two places:

• Monthly credits from your plan. They reset on the 1st of each month (UTC) and don't carry over.
• Purchased top-ups. They never expire, and are used after your monthly credits.

On the Free plan the Generate button is disabled while a run is in progress, and turns on again as soon as it finishes. See Pricing to upgrade. Paid plans are 30-day passes that you renew from that page.

Refunds.

• A run that fails, times out or produces no molecules is refunded in full automatically.
• You can cancel a run from the generate page. A run still waiting in the queue is refunded in full. A run that has started is refunded in proportion to the time not yet used, up to 80% of its cost.

API reference

Everything above is available over a REST API, so you can script runs. API access is included in the Max plan. Create a key in Settings, API keys (up to 5 active keys). The full key is shown once, so copy it then. API runs use the same credits and limits as the website. If your Max pass lapses, your keys stop working until you renew; they are not deleted.

Endpoints

Start a run

Example

# 1. Load a structure
curl -X POST https://targetgen-rjmtde.app.nearsite.cloud/v1/pdb/fetch \
  -H "X-Api-Key: tg_..." -H "Content-Type: application/json" \
  -d '{"pdb_id": "3POZ"}'

# 2. Find pockets (use the session_id from step 1)
curl https://targetgen-rjmtde.app.nearsite.cloud/v1/pdb/<session_id>/pockets -H "X-Api-Key: tg_..."

# 3. Start a run at a pocket centre
curl -X POST https://targetgen-rjmtde.app.nearsite.cloud/v1/jobs \
  -H "X-Api-Key: tg_..." -H "Content-Type: application/json" \
  -d '{"session_id": "<session_id>", "center": [12.4, 8.1, 22.7], "num_samples": 20}'

# 4. Poll until status is "done", then download
curl https://targetgen-rjmtde.app.nearsite.cloud/v1/jobs/<job_id> -H "X-Api-Key: tg_..."
curl https://targetgen-rjmtde.app.nearsite.cloud/v1/jobs/<job_id>/sdf -H "X-Api-Key: tg_..." -o molecules.sdf

import time, requests

BASE = "https://targetgen-rjmtde.app.nearsite.cloud/v1"
H = {"X-Api-Key": "tg_..."}

s = requests.post(f"{BASE}/pdb/fetch", headers=H, json={"pdb_id": "3POZ"}).json()["session_id"]
job = requests.post(f"{BASE}/jobs", headers=H, json={
    "session_id": s, "center": [12.4, 8.1, 22.7], "num_samples": 20,
}).json()["job_id"]

while True:
    r = requests.get(f"{BASE}/jobs/{job}", headers=H).json()
    if r["status"] in ("done", "failed"):
        break
    time.sleep(10)

print(r["status"], len(r.get("results", [])), "molecules")

Statuses and errors

A run's status is queued, running, done or failed. Errors use standard HTTP codes:

How it works

TargetGen chains four well-known tools. Knowing what each does helps you read the results.

Troubleshooting