RCSB Protein Data Bank: Enabling biomedical research and drug discovery

By David S. Goodsell, Christine Zardecki, L. D. Di Costanzo, Jose M. Duarte, B. Hudson, Irina Persikova, J. Segura, Chenghua Shao, Maria Voigt, John D. Westbrook and 2 more. Protein Science, 2019

303 citations recorded by the source corpus.

Analyses of publicly available structural data reveal interesting insights into the impact of the three‐dimensional (3D) structures of protein targets important for discovery of new drugs (e.g., G‐protein‐coupled receptors, voltage‐gated ion channels, ligand‐gated ion channels, transporters, and E3 ubiquitin ligases). The Protein Data Bank (PDB) archive currently holds > 155,000 atomic‐level 3D structures of biomolecules experimentally determined using crystallography, nuclear magnetic resonance spectroscopy, and electron microscopy. The PDB was established in 1971 as the first open‐access, digital‐data resource in biology, and is now managed by the Worldwide PDB partnership (wwPDB; wwPDB.org). US PDB operations are the responsibility of the Research Collaboratory for Structural Bioinformatics PDB (RCSB PDB). The RCSB PDB serves millions of RCSB.org users worldwide by delivering PDB data integrated with ∼40 external biodata resources, providing rich structural views of fundamental biology, biomedicine, and energy sciences. Recently published work showed that the PDB archival holdings facilitated discovery of ∼90% of the 210 new drugs approved by the US Food and Drug Administration 2010–2016. We review user‐driven development of RCSB PDB services, examine growth of the PDB archive in terms of size and complexity, and present examples and opportunities for structure‐guided drug discovery for challenging targets (e.g., integral membrane proteins).

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/96a3b6e16c3b8516607632dce9e3447942e5641c

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Andrej Sali
2. Shuchismita Dutta
3. Stephen K. Burley
4. Christine Zardecki
5. David S. Goodsell
6. John D. Westbrook
7. Alexander S. Rose
8. Valeria Molinero

In Molecular Biology

1. Andrej Sali
2. Catherine L. Lawson
3. Jose M. Duarte
4. Shuchismita Dutta
5. Stephen K. Burley
6. Christine Zardecki
7. David S. Goodsell
8. John D. Westbrook

In Spectroscopy

1. Andrej Sali
2. Stephen K. Burley
3. David S. Goodsell
4. Ben M. Webb
5. Jianlin Cheng

Citations in the corpus

• RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences (2020, background): “Looking ahead, the PDB archive houses structures of many human proteins that represent drug targets of tomorrow (2), thereby ensuring that structural biologists and structure-guided approaches will continue to facilitate discovery and development of lifechanging medicines for patients and their fami”
• AlphaFold2 models indicate that protein sequence determines both structure and dynamics (2022, background): “Proteins with structures deposited in the protein data bank 75 , even proteins with high-resolution X-ray structures, also contain significant disorder contents in their sequences 60,76 .”