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

Message from RCSB PDB

Molecular Biology Education Cover

Since 2000, the RCSB PDB Molecule of the Month series has introduced millions of visitors to the shape and function of the 3D structures archived in the Protein Data Bank. A recent article in BAMBed reflects on the history, usage, and community surrounding this key RCSB PDB series.

Insights from 20 years of the Molecule of the Month. David S. Goodsell, Christine Zardecki, Helen M. Berman, Stephen K. Burley
(2020) BAMBed 48: 350-355 doi:10.1002/bmb.21360

Goodsell’s column for January 2020 offers a personal meditation on the growing revolution in structural biology that provides these amazing glimpses into biology.

Coronavirus Lifecycle Painting

Coronavirus Life Cycle by David S. Goodsell, RCSB PDB; doi: 10.2210/rcsb_pdb/goodsell-gallery-023

Since the release of the first PDB structure from SARS-CoV-2 (PDB structure 6lu7), educational materials including molecular landscape paintings, downloadable illustrations, and a video demonstrating the effects of hand washing at the molecular level have been released into a Coronavirus Collection at PDB-101.

A new publication describes scientific sources used in the creation of the painting Coronavirus Life Cycle, and provides examples of the digital dissemination of this painting and related materials and a discussion of the public response.

Integrative illustration for coronavirus outreach. David S. Goodsell, Maria Voigt, Christine Zardecki, Stephen K. Burley
(2020) PLoS Biol 18: e3000815. doi:10.1371/journal.pbio.3000815

Explore the collection of coronavirus-related educational materials at PDB-101.

Drug Discovery Today Cover

Cover art by Maria Voigt, RCSB PDB

The feature story in the May issue of Drug Discovery Today outlines how open access to 3D macromolecular structure information managed by the Protein Data Bank facilitated discovery and development of >90% of new antineoplastic agents approved by the FDA 2010–2018.

Impact of the Protein Data Bank on antineoplastic approvals. John D.Westbrook, Rose Soskind, Brian P. Hudson, Stephen K.Burley
(2020) Drug Discovery Today 25: 837-850 doi:10.1016/j.drudis.2020.02.002

Detecting Shape Similarity

Real time structural search of the Protein Data Bank

A new paper describes a novel method that detects similarity between protein shapes and that works equally fast for any size of proteins or assemblies. This method drives the Structure Similarity option in Advanced Search. Users can search for similar polymeric chains to a given chain or assemblies to a given assembly.

Real time structural search of the Protein Data Bank
Dmytro Guzenko, Stephen K. Burley, Jose M. Duarte
(2020) PLoS Comput Biol 16: e1007970. doi: 10.1371/journal.pcbi.1007970

New SARS-CoV-2 PDB structures and related resources are updated regularly at

Corona virus 3D model
Snapshot: October 1, 2020
169,436 Released atomic coordinate entries
Molecule Type
148,632 Proteins, peptides, and viruses
3454 Nucleic acids
8753 Protein/nucleic acid complexes
8597 Other
Experimental Technique
150,014 X-ray
13,133 NMR
6,008 Electron Microscopy
175 Multi Method
69 Neutron Diffraction
37 Other