Protein Data Bank at Rutgers impacts research, education and drug discovery

Jun 21 2018

When Jimmy Carter was diagnosed with end-stage metastatic melanoma in 2015, he began taking a drug developed in part using 3D molecular data. Insights like these into drug discovery and other fields of scientific research are possible using the 140,000-plus 3D molecular structures made freely available in the RCSB Protein Data Bank at Rutgers University–New Brunswick.

Today, the former president's cancer is in remission thanks partly to anti‐cancer therapies developed through understanding the 3D structure of a protein that stimulates the immune system to attack and kill cancer cells. In biology, function follows form, meaning knowledge of shape (3D structure) explains how proteins work in our bodies and how they contribute to health and disease.

"The Protein Data Bank has transformed biology and medicine by impacting research, education and drug discovery," said Stephen K. Burley, University Professor and Henry Rutgers Chair at Rutgers–New Brunswick, who directs the RCSB Protein Data Bank and the Institute for Quantitative Biomedicine. "It is a global public good that accelerates scientific advances. Indeed, the chance of winning a Nobel Prize in chemistry is disproportionately higher if you are a practitioner of the sciences that contribute 3D structural data to the Protein Data Bank."

The globally unique data bank – the first open-access, digital data resource in biology – is managed by the Worldwide Protein Data Bank partnership between data centers in the U.S., Europe and Asia. U.S. operations are led by Rutgers and the University of California, San Diego-San Diego Supercomputer Center. Funding comes from the National Science Foundation, National Institutes of Health and U.S. Department of Energy. The data bank has a long history with Rutgers. Helen M. Berman, Board of Governors distinguished professor emerita of chemistry and chemical biology at Rutgers–New Brunswick, co-founded the data bank in 1971 and brought it to Rutgers in 1998. She continues to provide support in her role as director emerita.

"Virtually everything that happens inside a cell in any living organism is carried out by a protein, and knowledge of that protein's 3D structure tells you how the protein works," Burley said. "Function is a direct consequence of 3D shape, and once nature finds a strategy that works as a molecular machine, it tends to stick with it throughout evolution."

Every year, more than 1 million users tap into RCSB Protein Data Bank resources online. They include people studying basic biology, biomedicine, computer science, math, physical sciences, materials science, biomedical engineering, bioenergy and renewable energy. The data bank's education and outreach website, PDB-101, attracts more than 600,000 users annually.

"Drug companies and the U.S. Food and Drug Administration are also big Protein Data Bank users because 3D structures of proteins enable and accelerate discovery and development of new drugs," Burley said. "Use of the Protein Data Bank is also helping in the fight against antibiotic resistance, a major global public health problem. We understand how antibiotic resistance happens at the molecular and atomic levels because of 3D structures in the data bank."

If the data bank archive vanished, we would lose more than $13 billion worth of valuable research data, according to a 2017 analysis. The economic impact of RCSB Protein Data Bank services is estimated at more than $5.5 billion a year – 800 times the operating costs of the resource.

"That number doesn't include the societal benefits of new drugs coming from the biopharmaceutical industry, which maintains copies of the archive for daily use by researchers operating inside company firewalls," Burley said.