Newswise — Rutgers University-New Brunswick scientists Stephen Burley and Sagar Khare are available to speak to the press and provide background on the Nobel Prize in Chemistry 2024 awarded to David Baker, Demis Hassabis and John M. Jumper “for protein structure prediction.”
Stephen Burley, a University Professor and Henry Rutgers Chair, is a structural biologist, physician and data scientist. He directs the Research Collaboratory for Structural Bioinformatics Protein Data Bank, the Rutgers-based U.S. data center for a global archive of 3D structure data for proteins and DNA and RNA sequences. Burley also heads the Institute for Quantitative Biomedicine, which provides analytical tools for biomedical research.
Reporters may use this quote from Prof. Burley:
"The contents of the Protein Data Bank were used by Baker's Rosetta Fold and Google Deep Mind's AlphaFold. Without the Protein Data Bank, the advances made by David Baker and the Google Deep Mind Team would not have been possible."
Sagar Khare is a Professor in the Rutgers School of Arts and Science’s Department of Chemistry and Chemical Biology. His research is in the area of computational design of novel proteins – in particular enzymes, with applications in bioremediation and synthetic biology. He also was involved in developing tools for design as a postdoctoral fellow in David Baker’s lab.
Background on the Protein Data Base:
Experimentally-determined 3D biostructure information is distributed on an open-access basis by a singular global data resource, known as the Protein Data Bank (PDB). When the PDB was established in 1971 as the first open-access digital data resource in biology, it housed only seven protein structures.
Today, the PDB is regarded as a global public good vital to basic and applied research and education/training across the biological and biomedical sciences. In the spring of 2024, the PDB housed >225,000 experimentally determined, atomic-level 3D structures of biological macromolecules (i.e., proteins, DNA, and RNA), many of which have been visualized in the act of binding one or more small-molecule ligands, including United States Food and Drug Administration (US FDA) approved drugs.
Since 2003, the PDB has been managed jointly according to the FAIR Principles of Findability-Accessibility-Interoperability-Reusability by the Worldwide Protein Data Bank (wwPDB) partnership, including the US Research Collaboratory for Structural Bioinformatics Protein Data Bank or RCSB PDB, Protein Data Bank in Europe, Protein Data Bank Japan, Protein Data Bank China, Biological Magnetic Resonance Data Bank, and the Electron Microscopy Data Bank.
The RCSB PDB (RCSB.org) headquartered at Rutgers, The State University of New Jersey (with additional performance sites at the University of California San Diego and the University of California San Francisco) serves as the US wwPDB data center and as the wwPDB-designated Archive Keeper for the PDB.
Computed structure models (predicted structures or CSMs) of proteins generated using Rosetta Fold and AlphaFold are comparable in accuracy to lower-resolution experimentally-determined 3D structures of proteins.
The RCSB PDB RCSB.org research-focused web portal distributes both PDB data and more than 1 million CSMs generated using Rosetta Fold and AlphaFold.
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