| [wwPDB] Enhanced Collection of Starting Models A new PDBx/mmCIF category, _pdbx_initial_refinement_model has been introduced to improve information collected about starting model for X-ray, 3DEM and NMR methods. Experimentally derived vs computed models will be distinguished. Provenances of the ... |
| [wwPDB] Structure Predictors: Use ModelCIF for Computed Structure Models ModelCIF (GitHub) is a data information framework developed for and by computational structural biologists to describe structural models of macromolecules derived from computational methods. It provides an extensible data representation for deposition, ... |
| [wwPDB] PDB Reaches a New Milestone: 200,000+ Entries Depositors: Download this image, write the number of structures deposited, and tag us in your photos With this week's update, the PDB archive contains a record 200,069 entries. The archive passed 150,000 structures in 2019 and 100,000 structures in ... |
| [wwPDB] Time-stamped Copies of PDB and EMDB Archives A snapshot of the PDB Core Archive as of January 2, 2023 is available. A snapshot of the PDB Core archive (ftp://ftp.wwpdb.org, https://s3.rcsb.org/) as of January 02, 2023 has been added to ftp://snapshots.wwpdb.org, https://s3snapshots.rcsb.org ( ... |
| [wwPDB] PDB Certified as a Global Core Biodata Resource The Global Biodata Coalition (GBC) today announced that the Protein Data Bank (PDB) archive is included in the first list of Global Core Biodata Resources (GCBRs)—a collection of 37 resources whose long term funding and sustainability is critical to life ... |
| About PDBMLplus, PDBMLadd, and mmjson-plus We already finished providing PDBMLplus files written in the XML format. Instead, please use PDBj Mine RDB search or the mmjson-plus files written in json format. Introduction Before we provided PDBMLplus as the merged data of PDBML, XML-formatted PDB ... |
| [wwPDB] wwPDB Charter: Full and Associate Members Founded in 2003, the Worldwide Protein Data Bank (wwPDB) is dedicated to archiving, management, and public dissemination of structural biology data, and is committed to the FAIR Principles (Findability, Accessibility, Interoperability, Reusability) that ... |
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| [wwPDB] Future Planning: PDB entries with extended CCD or PDB IDs will be distributed in the PDBx/mmCIF format only wwPDB, in collaboration with the PDBx/mmCIF Working Group, has set plans to extend the length of accession codes (IDs) for PDB and Chemical Component Dictionary (CCD) entries in the future. PDB entries containing these extended IDs will not be supported by ... |
| [wwPDB] DNS name changes for PDB archive downloads from wwPDB wwPDB has introduced DNS names for programmatic access to PDB archive downloads: - FTP: ftp://ftp.wwpdb.org - HTTPS: https://files.wwpdb.org (replaces https://ftp.wwpdb.org) - RSYNC: rsync://rsync.wwpdb.org (replaces rsync://wwpdb.org) The PDB ... |
| [wwPDB] Improved EM validation with Q-score Starting September 23, wwPDB validation of 3DEM structures for which there is both a model and an EM volume will include the Q-score metric (Pintilie, G., et al., 2020, Nat. Methods). This follows recommendations from the wwPDB/EMDB workshop on cryo-EM ... |
| [wwPDB] New Publication: PDBx/mmCIF Ecosystem An article on the PDBx/mmCIF Ecosystem is part of the Journal of Molecular Biology's special issue on Computational Resources for Molecular Biology 2022 A new article by the wwPDB and the PDBx/mmCIF Working Group describes the community-driven data ... |
| [wwPDB] Distributing PDBx/mmCIF-Formatted Assembly Files Starting May 3, 2022, the PDB archive distributes assembly files in PDBx/mmCIF format, allowing direct access and visualization of the curated assemblies for all PDB entries (original announcement). Previously, PDBx/mmCIF formatted assembly files ... |
| Protein Data Bank 50th Anniversary Virtual Issue: Featured structural articles from The Journal of Biochemistry were released We are pleased to announce the Protein Data Bank 50th Anniversary Virtual Issue: Featured structural articles from The Journal of Biochemistry were now released in The Journal of Biochemistry (JB). In this virtual issue, we celebrate the 50th ... |
| [wwPDB] ModelCIF Extension for Computed Structure Models ModelCIF, an extension of PDBx/mmCIF for computed structure models, is now available. The PDBx/mmCIF data standard underpins the Protein Data Bank (PDB) Core Archive, which is jointly managed by the worldwide Protein Data Bank (wwPDB) consortium. A ... |
| [wwPDB] CASP15 Call for Targets CASP (Critical Assessment of protein Structure Prediction) is in search for targets for the upcoming CASP15 modeling experiment (starting in May 2022). CASP community experiments aim to advance the state of the art in protein structure modeling. Every ... |
| [wwPDB] Deposition of Half-maps for Certain EM Entries Now Mandatory As announced previously, deposition of half-maps for single-particle, single-particle-based helical, and sub-tomogram averaging reconstructions to the EM Data Bank (EMDB) is mandatory as of February 25, 2022. This change is in response to a long-standing ... |
| The PDB 50th anniversary article was now released at The Journal of Biochemistry We are pleased to announce the PDB 50th anniversary article was now released at The Journal of Biochemistry. - Genji Kurisu, "Fifty years of Protein Data Bank in the Journal of Biochemistry", The Journal of Biochemistry, Volume 171, Issue 1, January ... |
| [wwPDB] Distributing PDBx/mmCIF-Formatted Assembly Files Starting May 3, 2022, the PDB archive will distribute assembly files in PDBx/mmCIF format, allowing direct access and visualization of the curated assemblies for all PDB entries. Currently, PDBx/mmCIF formatted assembly files are provided for structures ... |
| [wwPDB] Time-stamped Copies of PDB and EMDB Archives A snapshot of the PDB Core Archive (ftp://ftp.wwpdb.org) as of January 3rd, 2022 has been added to ftp://snapshots.wwpdb.org and ftp://snapshots.pdbj.org. A snapshot of the PDB Core archive (ftp://ftp.wwpdb.org) as of January 3, 2022 has been added ... |
| [wwPDB] Biocurator Milestone: >10,000 Depositions Processed RCSB PDB Biocurator Dr. Brian P. Hudson talking about the SARS-CoV-2 main protease in February 2020 Congratulations to the wwPDB biocurator Dr. Brian Hudson on processing over 10,000 PDB depositions! Dr. Hudson received his PhD in Chemistry from the ... |
| [wwPDB] Deposition of Half-maps for Certain EM Entries to Become Mandatory From February 25, 2022, deposition of half-maps for single-particle, single-particle-based helical, and sub-tomogram averaging reconstructions to the EM Data Bank (EMDB) will become mandatory. This change is in response to a long-standing community request ... |
| The announcement of PDB50 Anniversary Symposum in Asia PDBj poster prize winner PDBj successfully organized the PDB 50th Anniversary Symposium in Asia (online) on November, 24, 2021 with active participation of more than 300 international and local scientists. At the poster session, we had 78 poster presentations mainly from Asia, ... |
| [wwPDB] November Workshops on Open-Source Tools for Chemistry Join the Royal Society of Chemistry for two webinars on Protein Data Bank at 50: Accessing, Understanding, and Assessing PDB Data As part of their series of Workshops on Open-Source Tools for Chemistry, the Chemical Information and Computer ... |
| [wwPDB] Obituary for John Westbrook John Westbrook at the 2017 Congress and General Assembly of the International Union of Crystallography in Hyderabad, India John D. Westbrook Jr. (1957-2021), Research Professor at Rutgers University and Data & Software Architect Lead for the RCSB PDB, ... |
Info pages: 532 results
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PDB entries from 2024-04-17
