A recent study emphasizes this potential, showcasing the promise of citizen science in protein modeling. This innovative study was directed by Associate Professor Firas Khatib of the University of Massachusetts Dartmouth. Two gamers employed the web game Foldit to improve the original Protein Data Bank (PDB) model of yeast mitochondrial import inner membrane translocase subunit TIM44p. In particular, they targeted PDB entry 2fxt and made multiple impressive gains. This remarkable development represents a huge leap forward in the scientific community’s understanding of protein structures. We hope it raises awareness of the importance of collaborative, automated approaches to research.
This Foldit model improved the original structure substantially, maximising the number of β-strand/β-bridge residues from 48 to 56. Participants took advantage of the fully automated approaches, scripts, or “recipes” inside Foldit that involved no hands-on human guidance. This creative new model is a key step toward a future in which crowds of non-experts are able to make powerful contributions to complicated scientific problems.
Advances in Protein Modeling
Through a sequence of Foldit Reconstruction puzzles, this study examined how players advanced the state of the art. These puzzles were based on actual known protein structures. Scientists had long ago solved these structures using methods such as X-ray crystallography and cryo-electron microscopy, and they are readily available in the PDB.
In the original model, an Asp was the residue at a key position (indicated with a star). In the modified homology model, this variable amino acid was substituted with the fully conserved Gly388 residue. Furthermore, the players’ work led to a rearrangement of a surface loop, resulting in a register shift that enhanced the overall structure’s accuracy.
“Scientists across disciplines use the Protein Data Bank to guide experiments and develop new technologies. Even small errors in its models can lead to incorrect assumptions down the road. What’s exciting is that Foldit players have shown they can proactively improve these structures—strengthening the foundation for future research.” – Firas Khatib
The Role of Citizen Science
Foldit is a perfect example of how citizen science can let people who aren’t trained as biochemists help make important contributions to real science. Players use their creativity and critical thinking to find their way through elaborate protein architectures. On their designs, they suggest creative refinements that even experienced professionals would never think of.
This study serves as an important reminder of how models contained in the PDB need to be accurate. As arguably the world’s most important scientific resource, getting these models right is imperative. Researchers from multiple disciplines rely on this database to inform their experiments and technology creation. As the nation’s largest real estate portfolio holder, this means that any improvements can have monumental consequences.
The Foldit model continues to be successful by showing how gamifying science can truly inspire collaboration between a diverse group of players. Khatib has been personally involved with the Foldit project from its inception in 2008. He is passionate about getting more people involved in scientific research through fun and interactive platforms.
Implications for Future Research
Foldit’s innovations greatly improve on these models. They add beauty and depth to the larger dialogue around shared, more equitable, collaborative science. Through the combination of these automated methods with citizen engagement, researchers can explore new frontiers for scientific discovery.
If interest in citizen science keeps gaining momentum, these platforms—like Foldit—might become the new normal for how introductory research is performed across disciplines. The past players’ outcomes in this study vividly illustrate the potential of community engagement. Their engagement offers an unparalleled opportunity to move the scientific frontier and expand scientific knowledge.