wwPDB has introducing the first 3DEM Model-Map percentile slider (based on Q-score) to validation reports
Introducing the first 3DEM Model-Map percentile slider to the wwPDB validation report
Introducing the latest wwPDB Percentile slider based on the Q-score model-map validation metric
www.rcsb.org
September 26, 2025 at 4:44 PM
wwPDB has introducing the first 3DEM Model-Map percentile slider (based on Q-score) to validation reports
AlphaFold Server’s ligand menu just got a lot bigger and I almost missed it! You can now add any ligand from the wwPDB Chemical Component Dictionary. Just enter its CCD code 🥳
September 6, 2026 at 4:20 PM
AlphaFold Server’s ligand menu just got a lot bigger and I almost missed it! You can now add any ligand from the wwPDB Chemical Component Dictionary. Just enter its CCD code 🥳
"a PDB structure on hold will be scheduled for release if the wwPDB finds a bioRxiv preprint with matching authors, title, and an entry ID code" 👏 👏 👏
ht @katiecorker.bsky.social
www.wwpdb.org/news/news#67...
ht @katiecorker.bsky.social
www.wwpdb.org/news/news#67...
Deprecation of FTP File Download Protocol on November 1, 2024
wwPDB: Worldwide Protein Data Bank
www.wwpdb.org
November 13, 2024 at 9:43 PM
"a PDB structure on hold will be scheduled for release if the wwPDB finds a bioRxiv preprint with matching authors, title, and an entry ID code" 👏 👏 👏
ht @katiecorker.bsky.social
www.wwpdb.org/news/news#67...
ht @katiecorker.bsky.social
www.wwpdb.org/news/news#67...
Introducing the first 3DEM Model-Map percentile slider to the wwPDB validation report
From Oct 1, all new 3DEM entries will include the Q-score percentile slider — helping users quickly assess model–map fit quality across EMDB/PDB archives.
Read more: www.wwpdb.org/news/news?ye...
From Oct 1, all new 3DEM entries will include the Q-score percentile slider — helping users quickly assess model–map fit quality across EMDB/PDB archives.
Read more: www.wwpdb.org/news/news?ye...
wwPDB: 2025 News
wwPDB: Worldwide Protein Data Bank
www.wwpdb.org
September 24, 2025 at 9:08 AM
Introducing the first 3DEM Model-Map percentile slider to the wwPDB validation report
From Oct 1, all new 3DEM entries will include the Q-score percentile slider — helping users quickly assess model–map fit quality across EMDB/PDB archives.
Read more: www.wwpdb.org/news/news?ye...
From Oct 1, all new 3DEM entries will include the Q-score percentile slider — helping users quickly assess model–map fit quality across EMDB/PDB archives.
Read more: www.wwpdb.org/news/news?ye...
Today, @rcsbpdb.bsky.social introduces Q-score in EM validation reports. Q-score assesses model-map fit. A new percentile slider will compare an entry’s average Q-score to the full archive and a resolution-matched subset. This would help judge whether the fit is typical for the reported resolution.
Introducing the first 3DEM Model-Map percentile slider to the wwPDB validation report
Introducing the latest wwPDB Percentile slider based on the Q-score model-map validation metric
www.rcsb.org
October 1, 2025 at 12:25 AM
Today, @rcsbpdb.bsky.social introduces Q-score in EM validation reports. Q-score assesses model-map fit. A new percentile slider will compare an entry’s average Q-score to the full archive and a resolution-matched subset. This would help judge whether the fit is typical for the reported resolution.
Metalloproteins make up ~30% of the PDB archive.
To ensure FAIR data practices, wwPDB is remediating existing polyatomic metal-containing entries and CCDs — improving their chemical and coordination descriptions for better findability and reuse.
To ensure FAIR data practices, wwPDB is remediating existing polyatomic metal-containing entries and CCDs — improving their chemical and coordination descriptions for better findability and reuse.
October 28, 2025 at 2:43 PM
Metalloproteins make up ~30% of the PDB archive.
To ensure FAIR data practices, wwPDB is remediating existing polyatomic metal-containing entries and CCDs — improving their chemical and coordination descriptions for better findability and reuse.
To ensure FAIR data practices, wwPDB is remediating existing polyatomic metal-containing entries and CCDs — improving their chemical and coordination descriptions for better findability and reuse.
The effort adopts community tools like FindGeo (MetalPDB) and MetalCoord (CCP4).
Details and example files are available at wwPDB.org
.
For queries: info@wwpdb.org
Details and example files are available at wwPDB.org
.
For queries: info@wwpdb.org
wwPDB: Worldwide Protein Data Bank
wwPDB: Worldwide Protein Data Bank
wwPDB.org
October 28, 2025 at 2:43 PM
The effort adopts community tools like FindGeo (MetalPDB) and MetalCoord (CCP4).
Details and example files are available at wwPDB.org
.
For queries: info@wwpdb.org
Details and example files are available at wwPDB.org
.
For queries: info@wwpdb.org
wwPDB FTP area is no longer available (from Nov 1, 2024).
The RSYNC protocol hosted by wwPDB will continue.
More info:
www.wwpdb.org/news/news?ye...
Various database access options available from wwPDB and partners (RCSB, PDBe, PDBj, BMRB, EMDB):
www.wwpdb.org/ftp/pdb-ftp-...
The RSYNC protocol hosted by wwPDB will continue.
More info:
www.wwpdb.org/news/news?ye...
Various database access options available from wwPDB and partners (RCSB, PDBe, PDBj, BMRB, EMDB):
www.wwpdb.org/ftp/pdb-ftp-...
November 7, 2024 at 3:14 PM
wwPDB FTP area is no longer available (from Nov 1, 2024).
The RSYNC protocol hosted by wwPDB will continue.
More info:
www.wwpdb.org/news/news?ye...
Various database access options available from wwPDB and partners (RCSB, PDBe, PDBj, BMRB, EMDB):
www.wwpdb.org/ftp/pdb-ftp-...
The RSYNC protocol hosted by wwPDB will continue.
More info:
www.wwpdb.org/news/news?ye...
Various database access options available from wwPDB and partners (RCSB, PDBe, PDBj, BMRB, EMDB):
www.wwpdb.org/ftp/pdb-ftp-...
The wwPDB exhibit booth and related activities were made possible by the wwPDB Foundation, a 501(c)(3) nonprofit that supports outreach activities like poster and travel awards. Donate today and receive a special hemoglobin pin
wwPDB Foundation
wwPDB: Worldwide Protein Data Bank
foundation.wwpdb.org
August 15, 2026 at 3:58 PM
The wwPDB exhibit booth and related activities were made possible by the wwPDB Foundation, a 501(c)(3) nonprofit that supports outreach activities like poster and travel awards. Donate today and receive a special hemoglobin pin
Paper Published: Updated resources for exploring PDB structures and Computed Structure Models
Read about the RCSB PDB and other molecular biology databases in the annual Database Issue of Nucleic Acids Research
academic.oup.com/nar...
Read about the RCSB PDB and other molecular biology databases in the annual Database Issue of Nucleic Acids Research
academic.oup.com/nar...
Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank
Abstract. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB
academic.oup.com
January 21, 2025 at 5:12 PM
Paper Published: Updated resources for exploring PDB structures and Computed Structure Models
Read about the RCSB PDB and other molecular biology databases in the annual Database Issue of Nucleic Acids Research
academic.oup.com/nar...
Read about the RCSB PDB and other molecular biology databases in the annual Database Issue of Nucleic Acids Research
academic.oup.com/nar...
Announcement: Ligand Expo To Be Retired February 13, 2026
Users should transition to RCSB PDB and wwPDB services as soon as possible
Users should transition to RCSB PDB and wwPDB services as soon as possible
Announcement: Ligand Expo To Be Retired February 13, 2026
Users should transition to RCSB PDB and wwPDB services as soon as possible
www.rcsb.org
January 21, 2026 at 5:17 PM
Announcement: Ligand Expo To Be Retired February 13, 2026
Users should transition to RCSB PDB and wwPDB services as soon as possible
Users should transition to RCSB PDB and wwPDB services as soon as possible
Milestone reached: Over 20,000 new structures deposited to the PDB in 2025!
This reflects advances in cryo-EM, high-throughput crystallography, and AI-driven modelling, supported by expert wwPDB biocuration and open data sharing.
Read more: wwpdb.org/news/news?ye...
This reflects advances in cryo-EM, high-throughput crystallography, and AI-driven modelling, supported by expert wwPDB biocuration and open data sharing.
Read more: wwpdb.org/news/news?ye...
December 17, 2025 at 4:14 PM
Milestone reached: Over 20,000 new structures deposited to the PDB in 2025!
This reflects advances in cryo-EM, high-throughput crystallography, and AI-driven modelling, supported by expert wwPDB biocuration and open data sharing.
Read more: wwpdb.org/news/news?ye...
This reflects advances in cryo-EM, high-throughput crystallography, and AI-driven modelling, supported by expert wwPDB biocuration and open data sharing.
Read more: wwpdb.org/news/news?ye...
The wwPDB just hit a major milestone: 𝟏𝟎,𝟎𝟎𝟎 𝐄𝐌𝐃𝐁 𝐞𝐧𝐭𝐫𝐢𝐞𝐬 𝐫𝐞𝐥𝐞𝐚𝐬𝐞𝐝 𝐢𝐧 𝐚 𝐬𝐢𝐧𝐠𝐥𝐞 𝐲𝐞𝐚𝐫. To put this in context, the entire EMDB reached 10,000 entries total in 2019 — now the archive 𝐡𝐚𝐬 𝐬𝐮𝐫𝐩𝐚𝐬𝐬𝐞𝐝 𝟓𝟎,𝟎𝟎𝟎. Huge credit to the community driving 3DEM forward!
www.wwpdb.org/news/news?ye...
#3DEM #EMDB
www.wwpdb.org/news/news?ye...
#3DEM #EMDB
EMDB Surpasses 10,000 Entries in a Year
wwPDB: Worldwide Protein Data Bank
www.wwpdb.org
January 20, 2026 at 10:18 AM
The wwPDB just hit a major milestone: 𝟏𝟎,𝟎𝟎𝟎 𝐄𝐌𝐃𝐁 𝐞𝐧𝐭𝐫𝐢𝐞𝐬 𝐫𝐞𝐥𝐞𝐚𝐬𝐞𝐝 𝐢𝐧 𝐚 𝐬𝐢𝐧𝐠𝐥𝐞 𝐲𝐞𝐚𝐫. To put this in context, the entire EMDB reached 10,000 entries total in 2019 — now the archive 𝐡𝐚𝐬 𝐬𝐮𝐫𝐩𝐚𝐬𝐬𝐞𝐝 𝟓𝟎,𝟎𝟎𝟎. Huge credit to the community driving 3DEM forward!
www.wwpdb.org/news/news?ye...
#3DEM #EMDB
www.wwpdb.org/news/news?ye...
#3DEM #EMDB
The wwPDB has been featured this week by the Global Biodata Coalition! The wwPDB is a large freely-accessible repository of experimentally determined 3D structures of biological macromolecules.
⬇️Read more⬇️
www.linkedin.com/feed/update/...
⬇️Read more⬇️
www.linkedin.com/feed/update/...
January 27, 2025 at 1:21 PM
The wwPDB has been featured this week by the Global Biodata Coalition! The wwPDB is a large freely-accessible repository of experimentally determined 3D structures of biological macromolecules.
⬇️Read more⬇️
www.linkedin.com/feed/update/...
⬇️Read more⬇️
www.linkedin.com/feed/update/...
Winter Newsletter Published
Highlights the Target Zero documentary series, 2024 statistics, wwPDB news, and more.
In the Education Corner, learn about Molecule of the Month: Celebrating 25 Years of Storytelling and Announcing New Beginnings
cdn.rcsb.org/rcsb-pd...
Highlights the Target Zero documentary series, 2024 statistics, wwPDB news, and more.
In the Education Corner, learn about Molecule of the Month: Celebrating 25 Years of Storytelling and Announcing New Beginnings
cdn.rcsb.org/rcsb-pd...
RCSB PDB Quartely Newsletter | Winter 25 | Issue 104
This issue highlights the Target Zero documentary series, 2024 statistics, wwPDB news, and more
cdn.rcsb.org
January 15, 2025 at 5:12 PM
Winter Newsletter Published
Highlights the Target Zero documentary series, 2024 statistics, wwPDB news, and more.
In the Education Corner, learn about Molecule of the Month: Celebrating 25 Years of Storytelling and Announcing New Beginnings
cdn.rcsb.org/rcsb-pd...
Highlights the Target Zero documentary series, 2024 statistics, wwPDB news, and more.
In the Education Corner, learn about Molecule of the Month: Celebrating 25 Years of Storytelling and Announcing New Beginnings
cdn.rcsb.org/rcsb-pd...
As always with our Mycobacterial work, all cryo-EM maps and atomic models are scheduled for immediate release by the wwPDB (@rcsbpdb.bsky.social @pdbeurope.bsky.social etc)
October 30, 2025 at 4:12 PM
As always with our Mycobacterial work, all cryo-EM maps and atomic models are scheduled for immediate release by the wwPDB (@rcsbpdb.bsky.social @pdbeurope.bsky.social etc)
Want more biological database resources & tools in your feed?
Welcome EMBL-EBI (@ebi.embl.org) to 🦋💙 Bluesky 🦋💙!
PDBe is part of EMBL-EBI & behind various resources:
- founding partner of the wwPDB,
- community-led PDBe-KB resource
- AlphaFold Protein Structure Database
(with Google DeepMind)
Welcome EMBL-EBI (@ebi.embl.org) to 🦋💙 Bluesky 🦋💙!
PDBe is part of EMBL-EBI & behind various resources:
- founding partner of the wwPDB,
- community-led PDBe-KB resource
- AlphaFold Protein Structure Database
(with Google DeepMind)
Not enough bioinformatics in your Bluesky feed? We’ve got you covered. Follow us for our latest news, exciting life science research, updates from our data resources, new tools and training resources.
Haven't heard of EMBL-EBI? Take a look at what we’re working on. www.ebi.ac.uk/about/our-im...
Haven't heard of EMBL-EBI? Take a look at what we’re working on. www.ebi.ac.uk/about/our-im...
Our impact
We provide open data that helps scientists understand life and that informs solutions to real-world problems, such as infectious diseases, climate change and food security.
www.ebi.ac.uk
November 19, 2024 at 4:43 PM
Want more biological database resources & tools in your feed?
Welcome EMBL-EBI (@ebi.embl.org) to 🦋💙 Bluesky 🦋💙!
PDBe is part of EMBL-EBI & behind various resources:
- founding partner of the wwPDB,
- community-led PDBe-KB resource
- AlphaFold Protein Structure Database
(with Google DeepMind)
Welcome EMBL-EBI (@ebi.embl.org) to 🦋💙 Bluesky 🦋💙!
PDBe is part of EMBL-EBI & behind various resources:
- founding partner of the wwPDB,
- community-led PDBe-KB resource
- AlphaFold Protein Structure Database
(with Google DeepMind)
wwpdb is now quadruvirate - PDBChina was established recently
February 5, 2025 at 11:29 PM
wwpdb is now quadruvirate - PDBChina was established recently
Paper Published: 3DEM Structure-Map Validation Recommendations
Learn how wwPDB is addressing the challenge of validating 3DEM structures against primary map data
Learn how wwPDB is addressing the challenge of validating 3DEM structures against primary map data
Paper Published: 3DEM Structure-Map Validation Recommendations
Learn how wwPDB is addressing the challenge of validating 3DEM structures against primary map data
www.rcsb.org
August 25, 2025 at 4:22 PM
Paper Published: 3DEM Structure-Map Validation Recommendations
Learn how wwPDB is addressing the challenge of validating 3DEM structures against primary map data
Learn how wwPDB is addressing the challenge of validating 3DEM structures against primary map data
wwPDB has received a record number of depositions this year--more than 20,000!
Many thanks to all of our depositors and biocurators more making these important data available to all
Details:
Many thanks to all of our depositors and biocurators more making these important data available to all
Details:
Milestone: >20,000 Structures Deposited to the PDB in 2025
wwPDB has received a record number of depositions this year
www.rcsb.org
December 17, 2025 at 5:22 PM
wwPDB has received a record number of depositions this year--more than 20,000!
Many thanks to all of our depositors and biocurators more making these important data available to all
Details:
Many thanks to all of our depositors and biocurators more making these important data available to all
Details:
PDB-IHM (formerly PDB-Dev) is for integrative structures.
Intergrative structures = from multiple experimental & computational methods.
Since mid-2024 assigned PDB ids & DOIs.
Access via wwPDB archive or
PDB-IHM - pdb-ihm.org
👉 https://www.wwpdb.org/news/news?year=2025#677880ea44a8c95814022eb9
Intergrative structures = from multiple experimental & computational methods.
Since mid-2024 assigned PDB ids & DOIs.
Access via wwPDB archive or
PDB-IHM - pdb-ihm.org
👉 https://www.wwpdb.org/news/news?year=2025#677880ea44a8c95814022eb9
January 17, 2025 at 1:35 PM
PDB-IHM (formerly PDB-Dev) is for integrative structures.
Intergrative structures = from multiple experimental & computational methods.
Since mid-2024 assigned PDB ids & DOIs.
Access via wwPDB archive or
PDB-IHM - pdb-ihm.org
👉 https://www.wwpdb.org/news/news?year=2025#677880ea44a8c95814022eb9
Intergrative structures = from multiple experimental & computational methods.
Since mid-2024 assigned PDB ids & DOIs.
Access via wwPDB archive or
PDB-IHM - pdb-ihm.org
👉 https://www.wwpdb.org/news/news?year=2025#677880ea44a8c95814022eb9
wwPDB Foundation Poster Prize at Protein Society Meeting
Congratulations to Gayathri Ayyar Manjula (Northeastern) for Structure Based Analysis to Distinguish Canonical Enzymes, Noncanonical Enzymes & Catalytically Inactive Pseudoenzymes in an Enzyme Superfamily
www.rcsb.org/news/fe...
Congratulations to Gayathri Ayyar Manjula (Northeastern) for Structure Based Analysis to Distinguish Canonical Enzymes, Noncanonical Enzymes & Catalytically Inactive Pseudoenzymes in an Enzyme Superfamily
www.rcsb.org/news/fe...
September 30, 2026 at 7:22 PM
wwPDB Foundation Poster Prize at Protein Society Meeting
Congratulations to Gayathri Ayyar Manjula (Northeastern) for Structure Based Analysis to Distinguish Canonical Enzymes, Noncanonical Enzymes & Catalytically Inactive Pseudoenzymes in an Enzyme Superfamily
www.rcsb.org/news/fe...
Congratulations to Gayathri Ayyar Manjula (Northeastern) for Structure Based Analysis to Distinguish Canonical Enzymes, Noncanonical Enzymes & Catalytically Inactive Pseudoenzymes in an Enzyme Superfamily
www.rcsb.org/news/fe...
wwPDB News: New tools support deposition of structures to the wwPDB PDB and 3DEM Core Archives directly from structure determination software packages
Upload structures to the wwPDB OneDep system directly from refinement software packages
www.rcsb.org/news/fe...
Upload structures to the wwPDB OneDep system directly from refinement software packages
www.rcsb.org/news/fe...
August 11, 2026 at 4:01 PM
wwPDB News: New tools support deposition of structures to the wwPDB PDB and 3DEM Core Archives directly from structure determination software packages
Upload structures to the wwPDB OneDep system directly from refinement software packages
www.rcsb.org/news/fe...
Upload structures to the wwPDB OneDep system directly from refinement software packages
www.rcsb.org/news/fe...
Interested in learning more about plans to extend PDB IDs to 12 characters?
Watch this brief presentation by RCSB PDB biocurator Ezra Peisach
youtu.be/qXTCJ21cr9o...
Watch this brief presentation by RCSB PDB biocurator Ezra Peisach
youtu.be/qXTCJ21cr9o...
Supporting Extended PDB IDs
wwPDB anticipates that all four-character PDB IDs will be exhausted by 2028, after which 12-character PDB IDs will be issued. Entries with extended PDB IDs will not be compatible with the legacy PDB file format and will only be available in PDBx/mmCIF format. wwPDB encourages users to transition to
youtu.be
April 18, 2025 at 3:44 PM
Interested in learning more about plans to extend PDB IDs to 12 characters?
Watch this brief presentation by RCSB PDB biocurator Ezra Peisach
youtu.be/qXTCJ21cr9o...
Watch this brief presentation by RCSB PDB biocurator Ezra Peisach
youtu.be/qXTCJ21cr9o...