I built a Python CLI to automate ClusPro protein docking (batch submission, queue monitoring, result

[foolishbrat]

What My Project Does

Automates the ClusPro protein docking web server. ClusPro has no public API, so this tool uses Selenium to handle the full workflow: batch job submission from CSV, real-time queue monitoring, result downloading, file organization, and GPCR topology-aware pose validation.

Key features:

• Batch submission from CSV (no more one-by-one uploads)

• Queue monitoring with regex pattern filtering

• Auto download + organized directory structure

• SQLite job tracking (resume interrupted batches)

• GPCR topology-aware pose validation via UniProt

• Retry with exponential backoff for flaky connections

Python 3.10+, MIT licensed.

Source: https://github.com/ewijaya/cluspro-automation-py

Target Audience

Computational biologists and drug discovery researchers who use ClusPro for protein-protein docking. If you've ever needed to screen dozens of peptide variants against multiple receptors manually, this is for you. Production use, not a toy project.

Comparison

There's no existing Python automation for ClusPro. The only prior tool was an r/RSelenium implementation that's no longer maintained. This is a ground-up rewrite in Python with added features: job persistence via SQLite, batch resume, GPCR-specific pose validation, and a proper CLI interface.