Insights from the PDB

Last updated on Sun Feb 11 22:55:43 2024.

The Protein Data Bank (PDB) is a repository of experimentally determined three-dimensional structures of biological macromolecules (mostly proteins and nucleic acids). The structures it contains are very useful by themselves for answering biological questions, or for asking even more questions. In addition, the associated metadata (structure annotations) can also answer many interesting questions.

The PDB already provides statistics on some of its metadata, but these are very general in scope. The PDB in Europe (PDBe) provides programmatic access to the database through the PDBe API. By collecting appropriate metadata from the database, one can get much finer insight, for example specific to a particular field of structural biology.

This website presents the results of analyzing metadata from the Protein Data Bank to answer questions I am interested in. Some of these analyses are part of a series of posts on my blog; this website consolidates the results in a format that is easier to keep up-to-date and consult. I will add more analyses as I find the need. Each analysis indicates the date when it was last run, and I will try to update the entire site about once a month. If you notice it is out of date, feel free to contact me and I will update it.

You are free to use all figures and code used to generate them, provided you give credit appropriately.

Currently available analyses

• Nucleosome structures
• DNA length in protein-DNA complexes
• DNA length in structures of free DNA