Published quarterly by the Research Collaboratory for Structural Bioinformatics Protein Data Bank

In this Issue:

Message from RCSB PDB


Celebrating 50 Years of the PDB

The PDB was announced on October 20, 1971 in Crystallography: Protein Data Bank Nature New Biology 233: 223 (1971) doi:10.1038/newbio233223b0.

Fifty years later, the PDB archive contains >170,000 structures of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. It is managed by the Worldwide PDB (wwPDB) organization that ensures that the PDB is freely and publicly available to the global community.

Cover of the 2021 calendar

A new calendar available for download commemorates 50 years of the archive. Each month's image is available to be used as a virtual meeting background.

wwPDB will celebrate this golden anniversary with symposia and events throughout 2021.

Registration for the May 4-5 virtual symposium is now open. This event will include presentations from speakers from around the world who have made tremendous advances in structural biology and bioinformatics. Students and postdoctoral fellows are especially encouraged to attend and will be eligible for poster awards.

During this fiftieth anniversary year, consider supporting the PDB's spirit of openness, cooperation and education with a donation to the wwPDB Foundation.

The wwPDB Foundation was established in 2010 to raise funds in support of the outreach activities of the wwPDB. The Foundation raised funds to help support PDB40, a symposium celebrating the 40th anniversary of the archive; workshops; and educational publications. The Foundation is chartered as a 501(c)(3) entity exclusively for scientific, literary, charitable, and educational purposes.

2020 Publications

RCSB Protein Data Bank: Enabling biomedical research and drug discovery
(2020) Protein Science 29: 52-65 doi: 10.1002/pro.3730
D3R grand challenge 4: Blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies
(2020) Journal of Computer-Aided Molecular Design 580: 99–119 doi: 10.1007/s10822-020-00289-y

How to help the free market fight coronavirus
(2020) Nature 34: 167 doi: 10.1038/d41586-020-00888-7

Art and Science of the Cellular Mesoscale
(2020) Trends in Biochemical Sciences 45: 472-483 doi: 10.1016/j.tibs.2020.02.010
The TRUST Principles for digital repositories
(2020) Sci Data 7:144 doi: 10.1038/s41597-020-0486-7
Impact of the Protein Data Bank Across Scientific Disciplines
(2020) Data Science Journal 19:1-14 doi: 10.5334/dsj-2020-025
Impact of the Protein Data Bank on antineoplastic approvals
(2020) Drug Discovery Today 25:837-850 doi: 10.1016/j.drudis.2020.02.002
Insights from 20  years of the Molecule of the Month
(2020) BAMBed 48: 350-355 doi: 10.1002/bmb.21360
Real time structural search of the Protein Data Bank
(2020) PLoS Comput Biol 16: e1007970 doi: 10.1371/journal.pcbi.1007970
Integrative illustration for coronavirus outreach
(2020) PLoS Biol 18: e3000815 doi: 10.1371/journal.pbio.3000815
Virtual Boot Camp: COVID-19 evolution and structural biology
(2020) BAMBed 48:511–513 doi: 10.1002/bmb.21428
Real-time structural motif searching in proteins using an inverted index strategy
(2020) bioRxiv doi: 10.1101/2020.09.11.293977
RCSB Protein Data Bank tools for 3D structure-guided cancer research: human papillomavirus (HPV) case study
(2020) Oncogene 39: 6623–6632 doi: 10.1038/s41388-020-01461-2
BinaryCIF and CIFTools—Lightweight, efficient and extensible macromolecular data management
(2020) PLOS Computational Biology 16: e1008247 doi: 10.1371/journal.pcbi.1008247
High-performance macromolecular data delivery and visualization for the web
(2020) Acta Cryst D76: 1167-1173 doi: 10.1107/S2059798320014515
Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first six months of the COVID-19 pandemic
(2020) bioRxiv 2020.12.01.406637; doi: 10.1101/2020.12.01.406637

New SARS-CoV-2 PDB structures and related resources are updated regularly at rcsb.org/covid19

Corona virus 3D model
Snapshot: January 1, 2021
173,005 Released atomic coordinate entries
Molecule Type
151,623 Proteins, peptides, and viruses
3,501 Nucleic acids
9,012 Protein/nucleic acid complexes
8,869 Other
Experimental Technique
152,819 X-ray
13,227 NMR
6,674 Electron Microscopy
179 Multi Method
69 Neutron Diffraction
37 Other