“Every atom had its own punch card”

Interview with Helen Berman: The huge protein database that spawned AlphaFold and biology’s AI revolution, Nature, 18 October 2024.

PDB is an important database of protein structures. I’ve always thought the file format (.pdb) was unusual—not bad unusual, just a fun and quirky.

I now have a glimpse of why:

Q: How did scientists share protein structures before the PDB?

A: The PDB came into existence when there were only a handful of structures to begin with. They were shared either by punch cards — every atom had its own punch card — or magnetic tape. The individual investigator would have to mail those things across the ocean if it was going from England to America.

That was late 60s / early 70s, and 80 characters cards and readable encoding was in. It hasn’t changed that much.