Molecule of the Month: Fifty Years of Open Access to PDB Structures
The Protein Data Bank is celebrating its golden anniversary!
Structural Biology Begins
Elusive Membrane Channels
New Ways of Seeing Molecules
Exploring the Structure
Experimental and Predicted Structures of Myoglobin
As I write this article, the structural biology community is being transformed by the recent successes of AlphaFold2 and RoseTTAFold, which show a quantum leap in success rates for protein structure prediction. The example shown here is an easy one: the structure of human myoglobin predicted by AlphaFold2 (blue) is almost identical to the historic structure of whale myoglobin from Kendrew's laboratory (green, PDB ID 1mbn) and later structures of human myoglobin (click on the image for an interactive JSmol). Of course, there's only one reason that this structure is easy to predict: all predictive methods build on decades of structures available in the PDB archive. These predictive methods are a triumph of clever computing. They are also a triumph for the tens of thousands of researchers who have contributed to the PDB archive. The breadth of structural knowledge that is encompassed by their entries, and their willingness to make their structures freely available in the archive, made all this possible.
The same is true for the fields of drug discovery and development, vaccine development, enzyme engineering, bionanotechnology, and dozens more--all build on this goldmine of structural data to understand the basic principles of biomolecules, then apply them for new, breakthrough goals. Today, building on an explosion of new structure-determination techniques, the archive continues to grow rapidly. Who knows what will be possible? Exciting times are certainly ahead for the next 50 years of the PDB!
Topics for Further Discussion
- If you want to learn more about the history of the PDB, take a look at this Timeline of PDB History.
- Many publications and educational materials celebrating the PDB50 anniversary are available on the RCSB PDB website.
October 2021, David Goodsellhttp://doi.org/10.2210/rcsb_pdb/mom_2021_10