[3dem] PDB Reaches a New Milestone: 200,000+ Entries
Justin Flatt
justin at rcsb.rutgers.edu
Wed Jan 11 06:46:16 PST 2023
With this week's update, the PDB archive contains a record 200,069
entries. The archive passed 150,000 structures in 2019 [1] and 100,000
structures in 2014 [2].
Established in 1971, this central, public archive has reached this
critical milestone thanks to the efforts of structural biologists
throughout the world who contribute their experimentally-determined
protein and nucleic acid structure data.
wwPDB data centers support online access to three-dimensional structures
of biological macromolecules that help researchers understand many
facets of biomedicine, agriculture, and ecology, from protein synthesis
to health and disease to biological energy. Many milestones have been
reached since the archive released the 100,000th structure in 2014. PDB
data have been seminal in understanding SARS-CoV-2, and provided the
foundation for the development of AI/ML techniques for predicting
protein structure. The 50th anniversary of the PDB was celebrated
throughout 2021 [3].
Today, the archive is quite large, containing more than 3,000,000 files
related to these PDB entries that require more than 1086 Gbytes of
storage. PDB structures contain more than 1.8 billion non-hydrogen
atoms.
FUNCTION FOLLOWS FORM
In the 1950s, scientists had their first direct look at the structures
of proteins and DNA at the atomic level. Determination of these early
three-dimensional structures by X-ray crystallography ushered in a new
era in biology-one driven by the intimate link between form and
biological function. As the value of archiving and sharing these data
were quickly recognized by the scientific community, the Protein Data
Bank (PDB) was established as the first open access digital resource in
all of biology by an international collaboration in 1971 with data
centers located in the US and the UK.
Among the first structures deposited in the PDB were those of myoglobin
and hemoglobin, two oxygen-binding molecules whose structures were
elucidated by Chemistry Nobel Laureates John Kendrew and Max Perutz.
With this week's regular update, the PDB welcomes 266 new structures
into the archive. These structures join others vital to drug discovery,
bioinformatics and education.
The PDB is growing rapidly, increasing in size ~13% since 2011. In 2022,
an average of 275 new structures were released to the scientific
community each week. The resource is accessed hundreds of millions of
times annually by researchers, students, and educators intent on
exploring how different proteins are related to one another, to clarify
fundamental biological mechanisms and discover new medicines.
TWENTY YEARS OF COLLABORATION
Since its inception, the PDB has been a community-driven enterprise,
evolving into a mission critical international resource for biological
research. The wwPDB partnership was established in July 2003 with PDBe,
PDBj, and RCSB PDB. Today, the collaboration includes partners BMRB
(joined in 2006) and EMDB (2021).
The wwPDB ensures that these valuable PDB data are securely stored,
expertly managed, and made freely available for the benefit of
scientists and educators around the globe. wwPDB data centers work
closely with community experts to define deposition and annotation
policies, resolve data representation issues, and implement community
validation standards. In addition, the wwPDB works to raise the profile
of structural biology with increasingly broad audiences.
Each structure submitted to the archive is carefully curated by wwPDB
staff before release. New depositions are checked and enhanced with
value-added annotations and linked with other important biological data
to ensure that PDB structures are discoverable and interpretable by
users with a wide range of backgrounds and interests.
wwPDB eagerly awaits the next 100,000 structures and the invaluable
knowledge these new data will bring.
Links:
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[1] https://urldefense.com/v3/__https://www.wwpdb.org/news/news?year=2019*5c8c2db1ea7d0653b99c8774__;Iw!!Mih3wA!BvlP21H3QBc3MCTV8jL223kYoPPihZIA7tQS6jUlrKZw5VQLK7HJBv2VTabFdGC8oBaf_g1n0ZNZrn1vYkhRSHWQ$
[2] https://urldefense.com/v3/__https://www.wwpdb.org/news/news?year=2014*5764490799cccf749a90cdd6__;Iw!!Mih3wA!BvlP21H3QBc3MCTV8jL223kYoPPihZIA7tQS6jUlrKZw5VQLK7HJBv2VTabFdGC8oBaf_g1n0ZNZrn1vYm6o_bxM$
[3] https://urldefense.com/v3/__https://www.wwpdb.org/pdb50__;!!Mih3wA!BvlP21H3QBc3MCTV8jL223kYoPPihZIA7tQS6jUlrKZw5VQLK7HJBv2VTabFdGC8oBaf_g1n0ZNZrn1vYttzVdUL$
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