PDB-101

PDB-101
Name	PDB-101
Type	Educational portal
Owner	Research Collaboratory for Structural Bioinformatics
Launched	2011

PDB-101 is an educational portal associated with the Protein Data Bank that presents structural biology to students, educators, and the public through curated materials, visualizations, and teaching resources. It provides thematic guides, molecular art, and lesson plans that connect 3D macromolecular structures with topics in medicine, biochemistry, and molecular biology to support classroom instruction and informal learning. The portal interfaces with structural databases and community initiatives to promote literacy about biomolecular structure and function.

Overview

PDB-101 offers a user-friendly entry point to the Protein Data Bank ecosystem and the standards-driven infrastructure of the Worldwide Protein Data Bank consortium, integrating data contributions from institutions such as the European Molecular Biology Laboratory, RCSB PDB, PDBe, and PDBj. The site emphasizes visual communication through features like Molecule of the Month essays, instructional materials for teachers, and downloadable coordinate files consistent with formats adopted by projects such as MMTF and software from UCSF ChimeraX and PyMOL. It serves diverse audiences including students following curricula aligned with Next Generation Science Standards, educators at institutions like Harvard University and Massachusetts Institute of Technology, and researchers using tools developed at centers like the National Institutes of Health.

History and Development

PDB-101 originated from community efforts to make the Protein Data Bank accessible beyond specialized research groups, evolving alongside milestones in structural biology including the rise of X-ray crystallography, nuclear magnetic resonance spectroscopy, and cryo-electron microscopy. Early collaborators included the RCSB Protein Data Bank and the American Chemical Society, with design input from educators at universities such as Columbia University and University of California, San Francisco. Development cycles mirrored advancements in data standards from organizations like the International Union of Crystallography and software innovations from groups at Stanford University and University of Cambridge. Funding and support came from agencies including the National Science Foundation and the National Institutes of Health.

Content and Resources

The portal's signature feature, Molecule of the Month, profiles biomolecules by connecting structural coordinates to biomedical narratives involving topics such as hemoglobin in the context of sickle cell disease, hemagglutinin relating to influenza pandemic history, and enzymes implicated in Alzheimer's disease. Resources include downloadable teaching modules, 3D printable models adaptable to MakerBot and Ultimaker workflows, and animations compatible with platforms like YouTube and archival collections at the National Library of Medicine. Content is cross-referenced with entries in databases like UniProt, GenBank, and the Chemical Entities of Biological Interest ontology, and links to community initiatives including Open-Source Malaria and public health campaigns led by the World Health Organization.

Educational Programs and Outreach

PDB-101 supports workshops for K–12 teachers, summer programs for undergraduate students, and public exhibits coordinated with science centers such as the American Museum of Natural History and the Science Museum, London. Outreach collaborates with professional societies including the American Society for Biochemistry and Molecular Biology and the Biophysical Society to develop curricular materials aligned with pedagogy from institutions like the Carnegie Foundation for the Advancement of Teaching. Initiatives have included partnerships with citizen science projects such as Foldit and engagement at conferences like the Gordon Research Conferences and the Biophysical Society Annual Meeting.

Technical Infrastructure and Data Sources

The portal integrates structural data from the Protein Data Bank and metadata from the Worldwide Protein Data Bank archive, using standardized file formats developed by the International Union of Crystallography and compression strategies like Macromolecular Transmission Format. Visualization and dissemination pipelines rely on open-source software such as PyMOL, UCSF ChimeraX, and web frameworks maintained by developer communities at institutions like Rutgers University and University of California, San Diego. Data provenance traces to primary depositors at laboratories including Max Planck Institute for Biochemistry, Scripps Research, and national facilities like the Advanced Photon Source and National Center for CryoEM Access and Training.

Impact and Use Cases

PDB-101 informs classroom instruction at universities including Johns Hopkins University and University of Oxford, supports textbook authors and science communicators publishing with houses such as W. H. Freeman and Oxford University Press, and aids journalists reporting for outlets like Nature and Science. It has been used to generate illustrations for grant proposals to fund research at centers such as the Howard Hughes Medical Institute and to supply teaching materials for health education initiatives by the Centers for Disease Control and Prevention and vaccine research consortia. Academic studies have cited its role in increasing structural literacy among students and in facilitating interdisciplinary collaborations across institutions such as Yale University and University of Chicago.

Category:Structural biology