2024: A Year of Discovery and Development

When The Dark Protein Project launched in early 2024, it started as an crazy idea: that the world’s most powerful discoveries could come not from a handful of scientists, but from thousands of curious minds working together.

Over the past year, that idea became reality.

In just twelve months, our community grew from a small circle of beta testers to over 1,000 registered contributors across many countries. Together, they’ve helped annotate and analyze thousands of structural features across the dark proteome: the 90% of proteins whose functions remain unknown.

Building the Platform

In February, we released the first version of the Dark Protein web platform, complete with real-time annotation tools, visualized 3D models, and leaderboard tracking. The system now supports PDB-based protein exploration, binding-site prediction, and gamified labeling — transforming what used to be niche bioinformatics into a hands-on citizen science experience.

We partnered with data providers and open-source ML projects to make this possible, integrating models like ESM-2, Boltz-2, and AlphaFold into our backend pipeline for structural inference. Every labeled residue now feeds into a global dataset that powers our ongoing enzyme classification and pocket prediction studies.

Growing the Community

By mid-year, our series had connected students, hobbyists, and researchers across the world. Through collaborations with students and programs, contributors began mapping proteins linked to neglected diseases: from Wuchereria bancrofti to Trypanosoma cruzi.

Our first leaderboard challenge ended with hundreds of thousands of predictions verified by AI, setting the stage for our expansion into Level 2 and 3 datasets in 2025.

Looking Ahead

2024 was the year we built the foundation.
2025 will be the year we scale: with new missions on enzyme pathways, druggability scoring, and the next release of our AI-guided pocket analysis engine.

Each annotation brings the unknown a little closer to light.
Thank you to everyone who joined this journey, from our first thousand users to the scientists integrating our results worldwide.

Together, we’re mapping what life forgot.

— Shawnak Shivakumar