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The Protein Geometry Database: a new tool for researchers

The OSU Open Source Lab (OSL) and the OSU Department of Biochemistry and Biophysics have recently collaborated to create a database of protein geometry as a tool for researchers. Named the Protein Geometry Database (PGD), the database gives researchers robust and straightforward ability to analyze 16,000 non-redundant protein chains, their backbone conformation and geometry, as well as the relationships between them. OSU Professor and Chair of the Department of Biochemistry and Biophysics, Dr. Andrew Karplus, graduate student, Dr. Donnie Berkholz, and Postdoctoral Fellow, Dr. Dale Tronrud, provided the scientific knowledge for this first-of-its-kind program. OSL head software developer Peter Krenesky and OSL student developers John Davidson, Ani Ovsepyan, Sean Connell and Scott White supplied the technical skill.

“Proteins are important. Pretty much everything that happens in life, there's a protein for that,” says Karplus. “Proteins carry out their function because of their structure, so knowing how they look makes it easier to see what they do."

Dr. Karplus and his team had a rough version of the PGD before they approached the OSL for help, but searches through it could take hours. The database also had a fairly primitive user interface that was extremely difficult to use. The OSL team rewrote the PGD in Python using Biopython libraries, a set of freely available tools for biological computation. To deal with the congestion and overloading that occurred when statistical calculations were performed on the database, the developers used Django's aggregation functions to keep the data in one place while working with it.

The PGD is the first protein geometry database that analyzes protein geometry and conformation together. This results in more accurate angles, which allows researchers to create more accurate models of the protein's structure. “Deciphering how protein structure works and its linkage with function has important implications for our ability to understand how our body works at the smallest scale and to determine the molecular basis of diseases,” said Berkholz, who relied on the PGD's ability to complete complex, fast database searches to complete his thesis research.

Karplus and his team used the PGD to prove that protein bond angles depend on conformation. This brings to the field of protein structure a completely new level of understanding. You can learn more about their findings and the PGD in the following papers

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