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[wwPDB] wwPDB NMR restraint remediation conforms to standard NMR-STAR and NEF format

... chemical shifts and restraints have been deposited to the PDB - A valid topology file or specific comments must be ... _chemshifts/remediated_restraints). The existing data files in the PDB archive directories “nmr_chemical_shifts” and “nmr_restraints” ...

November 24, 2021 (Wed), "PDB50 Anniversary Symposium in Asia" will be held online

... -site data processing as a newly founded Asian hub for PDB data resource. Since 2001, PDBj has provided our newly developed ... Nakamura (Osaka University) 13:30-14:15 "50 years of PDB history in Asia" Genji Kurisu (Institute for Protein Research, Osaka ...

Support Fund for Protein Data Bank Japan

... were established to maintain and manage the PDB through international cooperation. The PDB is the only database that stores the ... ), to process data deposition, manage, and maintain the PDB under our collaboration. Protein Data Bank Japan The Protein ...

[wwPDB] Improved EM validation with Q-score

... wwPDB: https://ftp.wwpdb.org/pub/pdb/validation_reports/ - RCSB PDB: https://ftp.rcsb.org/pub/pdb/validation_reports/ - PDBe: https ... : https://ftp.wwpdb.org/pub/emdb/validation_reports/ - RCSB PDB: https://ftp.rcsb.org/pub/emdb/validation_reports/ - PDBj ...

Theoretical Models

... . Theoretical models are only available for download from the PDB FTP site as follows: - All theoretical models (current ... been removed from the PDB Contents Growth and PDB Holdings statistics. As of October 15, 2006, PDB depositions have been restricted ...

[wwPDB] A tribute to Prof. Michael G. Rossmann

... our own tribute to Michael and his contribution to the PDB archiving efforts. Michael has had an esteemed structural biology ... , with hundreds of his virus structures archived in the PDB. This includes the first structure determined of the human ...

Structure Navigator

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GIRAF

... in terms of the normalized GIRAF score ( score ). PDB The PDB ID of the hit. align The link to an alignment ... MSDChem database (except for polymeric molecules). protein Description of the PDB entry. score Normalized GIRAF score. This is a raw ...

[wwPDB] wwPDB EM Validation Reports Now Publicly Available

... wwPDB: ftp://ftp.wwpdb.org/pub/pdb/validation_reports/ - RCSB PDB: ftp://ftp.rcsb.org/pub/pdb/validation_reports/ - PDBe: ftp://ftp ... : ftp://ftp.wwpdb.org/pub/emdb/validation_reports/ - RCSB PDB: ftp://ftp.rcsb.org/pub/emdb/validation_reports/ - PDBj: ...

[wwPDB] Distributing PDBx/mmCIF-Formatted Assembly Files

... access and visualization of the curated assemblies for all PDB entries (original announcement). Previously, PDBx/mmCIF formatted ... assembly files provided for structures were non-PDB compliant, however the coordinates use model numbers to ...

About Asymmetric unit and Biological unit

... unit (i.e. non-crystallographic asymmetric unit) to the PDB. To reconstruct the biological assembly, non-crystallographic symmetry operations ... : non-large structures which don't excess the PDB format limitation PDB format (as in the past for a while) ...

[wwPDB] Distributing PDBx/mmCIF-Formatted Assembly Files

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News on 2012-09-20

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10,000 NMR structure milestone reached

... repository of experimental NMR data. NMR structures in the PDB and associated experimental data are presented by the wwPDB ... scientific community (Table 1). Future Challenges As the PDB archive continues to grow, the provision of robust validation ...

Promode help

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PDBML-extatom

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[wwPDB] From today: Mandatory PDBx/mmCIF format file submission for MX depositions

... /mmCIF is now the only format accepted for deposition of PDB structures resulting from macromolecular crystallography (MX), including X-ray, ... metadata supported by PDBx/mmCIF, compared to the legacy PDB format. PDB entries with 100,000 or more atoms, and ...

[wwPDB] Obituary for John Westbrook

... macromolecular machines, such as the ribosome, as single PDB structures (instead of split entries with atomic coordinates distributed ... I/HM structures, currently stored in the prototype PDB-Dev archive (pdb-dev.wwpdb.org), presented new challenges for data ...

News on 2010-05-06

... as part of the manuscript submission and review process. PDB validation reports are already required by the International Union ... . They contain essentially the same information, regardless of PDB annotation site. The validation reports will continue to be ...

[wwPDB] Modifications to support for SHEET and ligand SITE records in June 2021

... addition to PDBx/mmCIF files for all entries, wwPDB produces PDB format-formatted files for entries that can be represented in this ... records Restrictions in the SHEET record fields in legacy the PDB file format do not allow for the generation of complex ...

[wwPDB] ls-lR index file to be removed July 12, 2023

... JSON format, and can be found under the new /pdb/holdings/ archive tree. The inventory lists provided include: - ... - all_removed_entries.json.gz: a list of obsoleted PDB entries including information for entry authors, entry title, release date ...

News on 2009-01-23

... before remediation) ftp://snapshots.pdbj.org/20070731/ We will keep ftp://pdb.protein.osaka-u.ac.jp/v3/ as a symbolic link to ... . We will announce the release date for version 3.15 PDB archive when it will be confirmed. Sorry for your inconvenience ...

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