RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education

Abstract

The Protein Data Bank (PDB) is one of two archival resources for experimental data central to biomedical research and education worldwide (the other key Primary Data Archive in biology being the International Nucleotide Sequence Database Collaboration). The PDB currently houses >134,000 atomic level biomolecular structures determined by crystallography, NMR spectroscopy, and 3D electron microscopy. It was established in 1971 as the first open‐access, digital‐data resource in biology, and is managed by the Worldwide Protein Data Bank partnership (wwPDB; wwpdb.org). US PDB operations are conducted by the RCSB Protein Data Bank (RCSB PDB; RCSB.org; Rutgers University and UC San Diego) and funded by NSF, NIH, and DoE. The RCSB PDB serves as the global Archive Keeper for the wwPDB. During calendar 2016, >591 million structure data files were downloaded from the PDB by Data Consumers working in every sovereign nation recognized by the United Nations. During this same period, the RCSB PDB processed >5300 new atomic level biomolecular structures plus experimental data and metadata coming into the archive from Data Depositors working in the Americas and Oceania. In addition, RCSB PDB served >1 million RCSB.org users worldwide with PDB data integrated with ∼40 external data resources providing rich structural views of fundamental biology, biomedicine, and energy sciences, and >600,000 PDB101.rcsb.org educational website users around the globe. RCSB PDB resources are described in detail together with metrics documenting the impact of access to PDB data on basic and applied research, clinical medicine, education, and the economy.

Fabrication of three-dimensional proteinaceous micro- and nano-structures by femtosecond laser cross-linking

“…In this section, the protein properties that are necessary for cross-linking are discussed based on representative proteins chosen from the protein data bank (PDB) 73 , as indicated in Table 1. The role of BSA as a standard material and the function retention of cross-linked proteins are also addressed.…”

Structural biology data archiving – where we are and what lies ahead

“…In 1998, the Research Collaboratory for Structural Biology (RCSB) [12] took over the responsibility of running the PDB. Two years earlier, the Macromolecular Structure Database (MSD) had been established at a then still very young EMBL-EBI.…”

“…At present, over 200 downstream resources use PDB data [12]. Besides research-oriented databases, there are also educational resources for both students and scientists who are not specialists in structural biology, such as PDB-101 [12] and Proteopedia [30]. …”

Crystallographically correct but confusing presentation of structural models deposited in the Protein Data Bank

“…After all, the Protein Data Bank (PDB; Burley et al, 2018), as the principal repository of biologically relevant structures of macromolecules, serves not just crystallographers but chiefly researchers interested in the biological and biomedical aspects of the structures of macromolecules and their complexes. However, for the proper interpretation of many chemical and biological phenomena, such as various intermolecular interactions or the formation of biologically relevant assemblies, the whole content of the crystal unit cell should be presented in as compact as possible arrangement of individual molecules, preferentially in their proper oligomeric state.…”