More than $5 billion in funding has been provided by the National Institutes of Health (NIH) to structural biologists in the U.S. “It’s the first place I go when I need to create accurate illustrations of enzymes, DNA, ribosomes or just about any other biomolecule,” he said. ![]() “The PDB is an essential resource for education and outreach, providing a detailed look at the molecules that perform the processes of life,” he said.Īccording to Goodsell, who also serves as scientific outreach lead for the RCSB PDB, the companion portal provides materials that allow exploration of these structures by students, educators and the general public. “Importantly, the PDB showed the biological world how to think about, organize, collect and develop data into a useful ecosystem ─ this ecosystem shows the centrality of PDB data across different biological domains and scales.”Īnother “power” user of PDB is Artist/Scientist David Goodsell, a professor of computational biology at the Scripps Research Institute and a research professor at Rutgers University. ![]() “The PDB has been essential to much of my lab's work and countless others ─ we have used data from the PDB to gain important insights into the molecular piece parts of the SARS-CoV-2 virus, as well as used the data, together with molecular dynamics simulations, integrative modeling, and AI to understand how the viral spike protein opens,” said Amaro. One such user is Rommie Amaro, distinguished professor of theoretical and computational chemistry at UC San Diego. Researchers ranging from computational chemists to artists have utilized PDB for their work. “Thanks to open data and standards defined by the PDB, we have also witnessed the birth of a thriving sub-branch of bioinformatics known as structural bioinformatics, which is a direct consequence of the existence of the PDB.” “Not only does the PDB continue to showcase the power of open data and community, but more recently we are proving to be an enabler of a major AI breakthrough coined AlphaFold, which achieves highly accurate computational modeling of protein structures by learning from 50 years of data deposited at the PDB,” Duarte said. Site Lead Jose Duarte reflected on the ways in which this worldwide collaboration has transformed how scientists collect and share their structural biology data. In 1998, the RCSB PDB brought the PDB to UC San Diego – specifically to the San Diego Supercomputer Center (SDSC) on campus. data center for the global PDB archive, and makes PDB data available at no charge to all data consumers without usage limitations. Berman also established the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), which operates the U.S. The PDB was founded by Board of Governors Distinguished Professor Emerita of Chemistry and Chemical Biology Helen Berman at Rutgers-New Brunswick. ![]() In 50 years, it has gone from just seven protein structures within its data bank to more than 180,000 structures used worldwide by researchers to unlock the mysteries of human disease. Kimberly Mann Bruch and Cynthia Dillon, SDSC Communications Robin Lally, Rutgers UniversityĮstablished in 1971 as the first open access digital data resource for biology and medicine, the Protein Data Bank (PDB) is now a leading global resource for experimental data integral to scientific discovery. “Put another way, the PDB is so central to biological and biochemical research, it’s nearly impossible to imagine a world without it,” she said. Amaro explained that she and others have used PDB data to help guide computer-aided drug design methods, which are helping researchers more efficiently and effectively develop new and safer medications. ![]() UC San Diego's Distinguished Professor in Theoretical and Computational Chemistry Rommie Amaro and her team combined high-resolution PDB data with lower-resolution cryo-electron tomography data in order to model the SARS-CoV-2 virion in atomic detail. Statistics, Machine Learning & Predictive Analytics.
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