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Communications of the ACM


Plenty of Proteins

UCSD virtual reality environment

An interactive visualization of proteins from the Protein Data Bank in a virtual reality environment in the California Institute for Telecommunications and Information Technology at the University of California, San Diego.

Credit: UC San Diego

In biology, structure is important. The proteins that build our bones and skin, digest our food, replicate our DNA, and perform all manner of other tasks are built from amino acids, and fold themselves into shapes that dictate their behavior. For decades, structural biologists have been measuring and collecting protein structures and depositing them and their chemical formulas in a computer archive known at the Protein Data Bank.

What began in 1971 as a group of seven protein structures has ballooned to a collection of more than 107,000 biological macromolecule structures, with about 10,000 added annually. Many are much larger and contain much more information that the original seven, which creates new challenges for the computer scientists in charge of maintaining the archive. "Because the structures are so complex and the information is rich, the bigger structures now are so big that we had to move to a new format for archiving them," says Sameer Velankar, team leader of the content and integration group of the Protein Data Bank in Europe.


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