Protenix Server Automation — Chrome Extension

A Manifest V3 Chrome/Edge/Brave extension for submitting batches of Protenix JSON jobs through the Protenix web server. It follows the same one-click, on-page-progress approach as the sibling AlphaFold3_BrowserExt project while adapting the workflow to Protenix's upload form and post-submit Cloudflare verification.

What it does

• Loads one or more Protenix JSON files.
• Splits a top-level JSON array into individual jobs.
• Keeps the queue in local extension storage so navigation and verification pages do not lose progress.
• Selects Protenix's json upload mode, gives the file to the page's own JSON parser, and verifies that the form's Name field changed to the queued prediction name.
• After each navigation, gives the React form a short warm-up delay and polls for the Upload section for up to 30 seconds instead of failing on the first missing element.
• Automatically retries transient form-readiness, upload-import, model-control, and Submit-button misses up to four times with increasing delays; the JSON stays pending during those retries.
• Selects the requested Protenix model, optionally changes the page's Arco Use msa / Use template radio buttons, and presses Submit.
• Waits for the exact Submit the task review dialog. Its OK remains disabled until Turnstile succeeds; once Protenix enables it, the extension presses OK to send the server request.
• Waits for the exact Submitted successfully modal, clicks its OK button, and uses that modal as the authoritative completion signal.
• Detects Cloudflare/Turnstile verification and waits. It never attempts to solve, click, or bypass the check.
• Continues automatically after an automatic check; if Cloudflare asks for interaction, complete it yourself on the page.
• Shows a bottom-right progress panel with Stop, Resume, Previous JSON, and Next JSON controls.
• Lets you choose any earlier or later pending JSON as the next job without undoing or resubmitting completed work; the same controls are also in the popup.
• Lets you manually mark an unclear result as submitted or skip it without rebuilding the queue.
• Lets you return an unclear current JSON to pending after you verify it was not accepted, so an interrupted older queue can retry without being rebuilt.
• Includes a browser-only screening JSON generator for pairing fixed partner chains with a CSV of peptide/protein targets.
• Downloads a requested number of completed .tar.gz predictions from Prediction History, continuing across Arco pagination when necessary.

The default model is protenix_base_default_v1.0.0, which uses the AlphaFold 3-aligned 2021-09-30 structural-data cutoff. Change it in the popup when you want another Protenix checkpoint.

Install in Chrome

1. Open chrome://extensions.
2. Turn on Developer mode.
3. Click Load unpacked.
4. Select this Protenix_BrowserExt directory—the folder containing manifest.json.
5. Pin Protenix Automation from Chrome's extensions menu.

After editing the extension, return to chrome://extensions and click the reload icon on its card. Reload any already-open Protenix tabs so the updated page helper is present.

Submit a batch

1. Open the Protenix page that contains the JSON upload control, model selector, and Submit button.
2. Click the extension icon.
3. Choose one or more JSON files and click Add to queue.
4. Choose a model. MSA and Template default to Keep page setting because model variants have different feature support.
5. Click Start queue.
6. Watch the progress panel on the Protenix page.
7. If Cloudflare asks you to verify, complete the check yourself. The extension waits and continues after the page returns.

Use Previous JSON or Next JSON in the popup or page panel to change which pending file runs next. If a server submission is already active, that active job is left alone and the selected JSON becomes next in line.

If the server outcome cannot be identified confidently, the queue pauses. Check Protenix's job list, then choose Mark submitted + next or Skip current from the popup.

For a queue left active by an older extension version, first check Prediction History. If the named job is absent, use Retry current JSON; it returns that item to pending and selects it next. This action asks for confirmation because retrying a job that Protenix already accepted would create a duplicate.

After Protenix displays Submitted successfully, the extension records that named job as submitted, closes the success modal, waits for the configured inter-job delay, and reloads /model/prediction/add for the next queued job. Navigation to /model/prediction/history is also accepted as a fallback success signal.

Download completed predictions

1. Open Protenix Prediction History.
2. Open the extension popup.
3. Enter the number of result archives to download and click Download files.
4. Keep the history tab open while the bottom-right progress panel works through the visible table and subsequent pages.

Downloaded job URLs are remembered by path so repeated clicks continue with later results. Clear queue also clears that local download memory. Chrome may ask you to allow multiple downloads for protenix-server.com.

Generate screening jobs

1. Click Open JSON generator.
2. Paste the fixed receptor/partner sequence. Add additional fixed chains if necessary.
3. Load a CSV and select its target-name and target-sequence columns.
4. Click Generate.
5. Either add the jobs directly to the extension queue or download the JSON.

Generated jobs use this Protenix structure:

[
  {
    "name": "target_partner",
    "sequences": [
      { "proteinChain": { "sequence": "...", "count": 1 } },
      { "proteinChain": { "sequence": "...", "count": 1 } }
    ],
    "covalent_bonds": []
  }
]

For ligands, ions, modified residues, covalent bonds, or constraint-model inputs, prepare the JSON separately according to Protenix's official format and add it through the popup; the queue preserves each job object without rewriting it.

Safety and privacy

• The extension is limited to protenix-server.com pages.
• Input JSON and queue status remain in local Chrome extension storage until you clear the queue or remove the extension.
• No analytics or external requests are included.
• The extension uses the visible web form rather than private server APIs.
• Cloudflare verification is a user/server security boundary and is never bypassed.

Troubleshooting

• JSON upload mode not found — open the current Protenix submission page, not the task list or results page.
• Name field never changed after upload — Protenix's own JSON parser did not accept or finish loading that file; check the page's validation message before retrying.
• Form was not ready — the extension now waits and retries automatically. It pauses only after four full transient retries fail, so a slow page load no longer stops the batch immediately.
• Model option not found — select Keep the page selection, choose the model manually on Protenix, and restart the queue.
• Submit button is disabled — increase the delay only if the JSON visibly takes longer to load; otherwise inspect the page for a validation message.
• Outcome unclear — confirm whether the job appears in Protenix's task list, then use the manual resolution buttons.
• Only one archive downloads — allow multiple automatic downloads for Protenix when Chrome prompts, then retry the remaining count.
• The page changed after a Protenix update — stop the queue before retrying to avoid duplicate submissions. The label-based selectors in content.js are intentionally centralized for maintenance.

Files

manifest.json       Extension manifest and Protenix-only permissions
popup.html/css/js   Queue controls and submission settings
content.js          Page automation, persistent state, progress panel, Cloudflare wait
generator.html/css/js  Offline Protenix screening JSON builder
README.md           Installation and usage guide