Abstract
Since 1971, the Protein Data Bank (PDB) archive has served as the single, global repository for open access to atomic-level data for biological macromolecules. The archive currently holds >140,000 structures (>1 billion atoms). These structures are the molecules of life found in all organisms. Knowing the 3D structure of a biological macromolecule is essential for understanding the molecule’s function, providing insights in health and disease, food and energy production, and other topics of concern to prosperity and sustainability. PDB data are freely and publicly available, without restrictions on usage. Through bibliometric and usage studies, we sought to determine the impact of the PDB across disciplines and demographics. Our analysis shows that even though research areas such as molecular biology and biochemistry account for the most usage, other fields are increasingly using PDB resources. PDB usage is seen across 150 disciplines in applied sciences, humanities, and social sciences. Data are also re-used and integrated with >400 resources. Our study identifies trends in PDB usage and documents its utility across research disciplines.
Highlights
The Protein Data Bank (PDB) is the single, global repository for structural data of the molecules of life
Citing articles were found in all Essential Science Indicators (ESI) Subject Categories except Space Science; in particular, ESI categories Biology & Biochemistry, Chemistry, Molecular Biology & Genetics, and Computer Science contained the most citing articles
Keywords associated with structure determination and description were prevalent among citing publications in the early 2000s, but keywords pertinent to drug discovery, genetics and genomics, and most recently protein structure prediction have come to the fore
Summary
The Protein Data Bank (PDB) is the single, global repository for structural data of the molecules of life. Understanding the 3D structure of a biological macromolecule is essential for understanding critical areas of science, including fundamental biology, medicine, energy, drug discovery, and education. As an established archive that continues to grow in size, the PDB provides an opportunity to study the impact of PDB data and resources in these different areas. The PDB was established in 1971 to archive experimental data contributed by the new discipline of macromolecular crystallography, which was beginning to reveal three-dimensional (3D), atomic-level structures of biological macromolecules, including proteins, DNA, and RNA1,2. The PDB archives atomic coordinates and related experimental data from nuclear magnetic resonance spectroscopy and electron microscopy studies.
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