Federal science agencies renew and increase funding Rutgers’ Protein Data Bank

Federal funds totaling $49.4 million will underwrite core operations supporting the digital archive of protein structures.

Federal science agencies renewed and increased funding for a digital archive of protein structures housed by Rutgers University-New Brunswick.
The open-access data resource has enabled research in everything from agriculture to zoology and has laid the groundwork for Nobel Prize-winning discoveries.
Federal funds totaling $49.4 million will underwrite efforts at the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank through 2028, Rutgers officials said.
Grants from the U.S. National Science Foundation, the U.S. Department of Energy, the National Cancer Institute, the National Institute of Allergy and Infectious Diseases and the National Institute of General Medical Sciences of the National Institutes of Health will support the data bank.
The RCSB Protein Data Bank is a multi-institutional collaboration between Rutgers, the University of California San Diego and the University of California San Francisco.
Previous federal funding for RCSB Protein Data Bank core operations for 2019-2023 totaled $34.3 million.
“We are honored that so many scientific and medical achievements stemming from access to the data bank have been recognized for their profound impact on science and society,” University Professor and Henry Rutgers Chair Stephen Burley, director of the RCSB Protein Data Bank said. “We are excited at the prospect of enabling many more insights and innovations coming from global biological and biomedical research communities.”
The digital archive serves as the U.S. data center of the Worldwide Protein Data Bank partnership, which was established in 2003 to support joint management of the Protein Data Bank archive as a global public good.
Proteins are essential components of every cell in the body and play crucial roles in growth, repair and bodily functions. The shape or structure of each protein, essentially a string of atoms in an amino acid-chain molecule folded up in a complex fashion, determines its biological function.
Understanding the structures of proteins is central to molecular and cellular biology because it allows scientists to predict how the proteins will interact with other molecules, design drugs targeting specific proteins and gain insights into various biological processes and diseases.
To do all that, the structure itself needs to be discerned first at the atomic level. Proteins may be among the largest of the biomolecules, but they are still too small for the human eye to see, even with a conventional optical microscope. Before researchers can submit a protein structure to the database, they must employ painstaking methods coming from physics and chemistry to discern what the protein looks like. Some common methods used to study protein structures include X-ray crystallography, nuclear magnetic resonance imaging, 3D electron microscopy and cryo-electron tomography. Once deposited to the Protein Data Bank, the structure is rigorously validated and biocurated by experts.
Helen Berman, then a protein crystallographer at the Institute for Cancer Research, Fox Chase Cancer Center in Philadelphia, played a key role in co-founding the Protein Data Bank with colleagues in 1971. It was the first open-access, digital data resource in biology, designed to serve as the global archive for atomic-level, 3D structures of proteins and other large biomolecules.
Berman, now a Board of Governors Distinguished Professor Emerita of Chemistry and Chemical Biology at Rutgers-New Brunswick, brought the archive to Rutgers in 1998 and headed the effort until 2014.
The Protein Data Bank, continuously funded by the U.S. government for more than five decades, has grown to include more than 230,000 3D structures of proteins, nucleic acids (both DNA and RNA), viruses (the Zika virus, for instance), and macromolecular machines, such as the RNA polymerase II responsible for synthesizing messenger RNAs.
“When we first began to think about having a Protein Data Bank in the 1960s, there were only a handful of proteins whose structures had been determined, so, it was hard to imagine that more than 50 years later there would be more than 230,000,” Berman said. “My hope for the future is that having seen the enormous benefits of curating and archiving data, more scientific communities will follow the example of the Protein Data Bank.”
The database has more than fulfilled Berman’s vision, she said, proving to be an engine fueling scientific discovery. More than 60,000 scientists worldwide have freely contributed their data to the archive, and more than a million research papers have been published with discoveries and insights based on structures stored therein. About 10 million data files are downloaded from the Protein Data Bank daily by many millions of users working and learning in nearly every country and territory recognized by the United Nations.