462 new PDB entries have been released on 2025-06-11. 237423 entries are now available in total. Please refer to PDB / EMDB latest information for other updates.

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Now, we have released the PDBj Newsletter Vol.25.

- Vol.25 (March 2025) English (pdf 2.9M) / Japanese (pdf 3.2M) - Vol.24 (March 2024) English (pdf 2.9M) / Japanese (pdf 2.9M) - Vol.23 (March 2023) English (pdf 2.7M) / Japanese (pdf 3.0M) - Vol.22 No.2 (March 2022) English (pdf 2.4M) / Japanese (pdf 2.6M) ...

Newsletter Latest (Vol.25, 6 pages) - 日本語 English Previous news letters are here. Flyer for researchers (2 pages) - 日本語 English Leaflet for general people - 日本語 (A3 6 pages A4 12 pages) 2021 Calendar for celebrating 50th anniversary of PDB ...

PDB data is freely available for both commercial and non-commercial use (CC0 1.0 Universal Public Domain Dedication). For using other contents in PDBj site, see also the description below for details. You can freely link to any pages in our site ...

The wwPDB Foundation made an award for an outstanding student presentation at the 2025 Biophysical Society Meeting (February 15-19, Los Angeles, CA). Hsiang-Ling Huang Mechanisms of dysferlin-mediated membrane repair in health and disease Hsiang- ...

New version of PDB-IHM validation reports now include assessments of crosslinking mass spectrometry-based structure models We are pleased to announce the release of updated validation reports (version 2) for structures determined using integrative and ...

Please take this brief survey about the PDBx/mmCIF User Guide to help us gain insights into the Guide’s usage and identify areas for future improvement. Benefits of the PDBx/mmCIF ecosystem Your feedback is highly valued. Respondents can enter ...

Integrative structures are available at wwPDB.org and the PDB archive Structures of many large macromolecular assemblies are now being determined using integrative approaches, wherein information derived from multiple experimental and computational ...

New archive snapshots are available. A snapshot of the PDB Core archive (https://files.wwpdb.org/, https://s3.rcsb.org) as of January 1, 2025 has been added to https://s3snapshots.rcsb.org/, snapshots.rcsb.org (rsync -rlpy -a -v --delete snapshots. ...

PDB Chemical Component Dictionary (CCD) files with ideal geometries are now provided in SDF/MOL format at the PDB archive. Users can download individual CCD files in SDF/MOL format from the PDB archive at https://files.wwpdb.org/pub/pdb/refdata/chem_comp/. ...

This is the PDBj portal page for UniProt entries linking them with the structures in the PDB archive. The portal page provides an overview of the available PDB structures for a PDB entry, ranking them based on resolution and coverage. The UniProt ...

A new portal site that connects Japanese gene mutation information published in PDBj with protein sequences and structures (e.g., UniProt ID: P20813) The Protein Data Bank Japan (PDBj, head Prof. Genji Kurisu)*1, operated by the Institute for Protein ...

The FTP protocol for file downloads has been losing popularity over the years in favor of HTTP/S. There are many advantages of HTTP/S including speed, statelessness, security (HTTPS), and better support. Importantly during the past 2-3 years the main web ...

We will hold a luncheon seminar at APBJC 2024 (1st Asia & Pacific Bioinformatics Joint Conference ~JSBi, GIW, InCoB, APBC, and ISCB-Asia~) on Thursday, October 24, 2024. We look forward to seeing you there. Date 24th October 2024 (Thu) 12:30 - 13:30 ( ...

The Royal Swedish Academy of Sciences has announced that they will award David Baker, Demis Hassabis, and John Jumper the Nobel Prize in Chemistry 2024 for computational protein design and protein structure prediction. More than 60,000 PDB depositors ...

Preprint publications will trigger wwPDB data archive release The wwPDB releases entries under the following circumstances: - upon author’s request - upon publication - at the end of the hold period defined during submission (up to 1 year) if no ...

The PDB archive is now including annotation of protein chemical modifications (PCMs) and post-translational modifications (PTMs) in a standardized way. As previously announced, the PDBx/mmCIF dictionary has been extended to enhance PCM and PTM ...

Integrative structures are available at wwPDB.org and the PDB archive Structures determined by integrative and hybrid structure determination methods (IHM) are now available at wwPDB DOI landing pages for both released and on-hold entries, along with > ...

The FTP protocol for file downloads has been losing popularity over the years in favor of HTTP/S. There are many advantages of HTTP/S including speed, statelessness, security (HTTPS), and better support. Importantly during the past 2-3 years the main web ...

A workshop was held at EMBL-EBI (Hinxton, UK) in January 2020 to discuss data requirements for deposition and validation of cryoEM structures, with a focus on single-particle analysis and setting community recommendations. The outcomes of this meeting have ...

Structures determined by integrative and hybrid structure determination methods (IHM) are now available alongside experimental structures in the PDB archive. These structures are deposited into and processed by the PDB-Dev system. Each IHM structure is ...

Congratulations to biocurator Dr. Irina Persikova on processing over 10,000 PDB depositions. She is the seventh biocurator in the wwPDB reached this milestone. Irina has received Ph.D. training in Solid State Physics and provided over 20 years of ...

Benefits of the PDBx/mmCIF ecosystem We are excited to announce the launch of a detailed PDBx/mmCIF File Format User Guide. As the foundation for depositing, annotating, and archiving structural data across diverse experimental techniques, the ...