News

Benefits of the PDBx/mmCIF ecosystem

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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.

Integrative structures are available at wwPDB.org and the PDB archive

PDB-Dev now PDB-IHM

Structures of many large macromolecular assemblies are now being determined using integrative approaches, wherein information derived from multiple experimental and computational methods is combined to compute their three-dimensional structures.

New archive snapshots are available

Time-stamped Copies of PDB and EMDB Archives

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

Chemical Component Dictionary files with ideal geometries in SDF/MOL format are now available from the PDB archive

Access SDF/MOL formatted CCD files from the PDB archive

PDB Chemical Component Dictionary (CCD) files with ideal geometries are now provided in SDF/MOL format at the PDB archive.

New Ligand Pages: Revamped PDBeChem Service (Release)

PDBe team Introduces Novel Ligand Pages: A revamped PDBeChem service

The Protein Data Bank in Europe team is excited to announce the release of its enhanced PDBe-KB Ligand Pages

wwPDB News logo

wwPDB News: Deprecation of FTP File Download Protocol on November 1, 2024

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.

Illustration: A protein can consist of everything from tens of amino acids to several thousand (PDF)

The Nobel Prize in Chemistry 2024

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.

Preprint publications will trigger wwPDB data archive release

wwPDB Data Release Policy on Public Preprint Archives

The wwPDB releases entries under the following circumstances:

Examples PCM and PTM types

Annotation of protein modifications in the PDB

Protein chemical modifications (PCMs) and post translational modifications (PTMs) annotation is now included in CCD files, and updated atomic coordinate files are being rolled out.  

Integrative structures are available at wwPDB.org and the PDB archive

Access IHM structures at wwPDB DOI Landing Pages

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 >225,000 experimental structures in the PDB archive.

PDBe now hosts up-to-date Foldseek-compatible PDB database

PDBe launches Foldseek-compatible PDB collection for fast protein structure searches

Key highlights of the database The Protein Data Bank in Europe (PDBe) is excited to announce the availability of a new resource that will significantly enhance researchers'

Irina Persikova

Biocurator Milestone: >10,000 Depositions Processed

Congratulations to biocurator Dr. Irina Persikova on processing over 10,000 PDB depositions. She is the seventh biocurator in the wwPDB reached this milestone.