Launch of our renewed EDMap service Today we have launched the renewed EDMap service. The new version of EDMap shows the recently introduced wwPDB Electron Density Coefficient Files for new entries. For legacy entries, the old data is used, but with a revised implementation that improves ... |
What is the threshold to categorize as polymers for PDB entities? - FAQ Q) The molecule type for each entity is defined in entity.type. So what is the threshold to categorize as polymers for PDB entities? A) Currently, peptides with three or more residues and nucleotides with two or more bases are defined as polymers. But ... |
[wwPDB] Distribution of NMR data in a unified format at the PDB archive The wwPDB partners are pleased to announce that as of March 2020 the OneDep system will begin accepting upload of NMR experimental data as a single file, either in NMR-STAR or NEF format. This will start the transition from the current practice where ... |
[wwPDB] Time-stamped Copies of PDB and EMDB Archives A snapshot of the PDB Core archive (ftp://ftp.wwpdb.org) as of January 1, 2020 has been added to ftp://snapshots.wwpdb.org and ftp://snapshots.pdbj.org. Snapshots have been archived annually since 2005 to provide readily identifiable data sets for research ... |
[wwPDB] EMDB policy and procedures document now available A comprehensive policy and procedures document for the EMDB archive has been drawn up by the EMDB team in order to ensure consistent and coherent rules for its data. The document is now available to view on the EMDB website. Since its foundation in 2002 ... |
IPR seminar : PDBj-BINDS joint workshop on January 30, 2020 IPR seminar : PDBj-BINDS joint workshop “Protein and Compound Structural Data for Drug Discovery and Life Science” Purpose Structural data for proteins and compounds are useful for drug design and life science to know mechanisms of molecular interactions ... |
About the contents of the PDBj data site This page lists the files within the PDBj data archive. Information regarding data retrieval is written on the PDBj download page. Files within the data site efsite/data-web/${entryId}.mpbf.gz pdb_versionedShared between all wwPDB members data entries ... |
CiCLE workshop: sample evaluation for cryo-EM on January 6 or January 7, 2020 CiCLE workshop: sample evaluation for cryo-EM Outline:For obtaining high-resolution structures by single particle cryo-EM suitable sample evaluation and sample preparation is essential. An important aspect of sample evaluation is the effective use of ... |
[wwPDB] Additional EM map validation now available through OneDep The wwPDB validation reports provided in the OneDep system now have additional validation for electron microscopy (EM) maps to help users identify potential discrepancies in their data. The updated wwPDB validation reports in the OneDep system now ... |
PDBj Mine 2: SQL Search This page provides some examples of SQL queries that can be executed from the PDBj Mine interface at https://pdbj.org/rdb/search. You can use these samples at SQL Search of PDBj Mine or PDBj Mine:REST API. Documentation describing the SQL schema can be ... |
[wwPDB] Improved resolution of DOIs for PDB entries The wwPDB partners are pleased to announce an improved mechanism for the resolution of digital object identifiers (DOIs) associated with released PDB entries. We have launched new wwPDB landing web-pages for each released PDB entry. These pages present ... |
Encyclopedia of Protein Structures (eProtS) The service of Encyclopedia of Protein Structures (eProtS) is now under maintenance. |
On 24th Sep, we’ll hold a luncheon seminar at the Annual Meeting of the Biophysical Society of Japan in Miyazaki On 24th Sep, we will hold a luncheon seminar at the 57th Annual Meeting of the Biophysical Society of Japan in Miyazaki. Details are the following: Date 24th September 2019 (Tue) 11:30 - 12:20 (JST) Venue Seagaia Convention Center, Room G (IVORY) ... |
On 18th Aug (Sun), we exhibit a booth at the 29th Science Festa Osaka We'll exhibit a booth at the 29th Science Festa Osaka, which is a scientific event for young people. The exhibition day of our booth is only on 8/18 (Sun). We are going to exhibit the following menus: - Explanation of the basic for proteins - ... |
[wwPDB] Improve your previously released coordinates AND keep your original PDB ID with OneDep We are pleased to announce the availability of PDB versioning, allowing depositors to update their entries while retaining the same PDB accession code. Depositors can now submit new coordinates for existing entries. Initially, this is limited to PDB ... |
The release schedule of PDB data, the available data at each wwPDB site -FAQ Q) When are PDB entries released or updated? Can I download exactly the same PDB data from RCSB PDB, PDBe or PDBj? Is the update schedule different among them? A) The PDB data is updated on every 00:00 UTC (= 09:00 JST) of Wednesday at every site of ... |
Where is the XML Schema for the XML document for PDB? Q) Where is the XML Schema for the XML document for PDB? A) Please refer the following links for XML Schemas for PDBML and PDBMLadd. - PDBML - PDBMLadd [Back to the question list] |
PDB Entry Versioning On October 4th, 2017, the wwPDB introduced a versioning system to enable depositor-initiated or wwPDB-initiated updates to previously released PDB entries while retaining the same PDB accession code. A new FTP repository, now hosts versioned structural ... |
[wwPDB] From today: Mandatory PDBx/mmCIF format file submission for MX depositions From today, July 1st 2019, submission of PDBx/mmCIF format files for crystallographic depositions to the PDB is mandatory. PDBx/mmCIF is now the only format accepted for deposition of PDB structures resulting from macromolecular crystallography (MX), ... |
Data Deposition Information wwPDB OneDep System wwPDB OneDep system supports X-ray, EM and NMR structures. - Help for deposition wwPDB site: Tutorials wwPDB site: wwPDB OneDep System wwPDB site: wwPDB OneDep System FAQ wwPDB site: 5 Easy Steps to PDB Deposition with OneDep (PDF ... |
Data Format [PDBx/mmCIF] The PDBx/mmCIF format is modified format based on CIF (a file format used to describe crystal structures) and has been adapted for macromolecules. Both PDBx/mmCIF as well as CIF are based on the STAR format. The PDBx/mmCIF format will become ... |
PDBML [PDBML: XML for PDB] PDBML is one of the canonical XML formats converted from the PDBx/mmCIF format into XML. This format was first introduced in the following article: PDBML: the representation of archival macromolecular structure data in XML. ... |
PDBML-noatom PDBML-noatom files are the same as PDBML files except that there is noatom_siteCategoryelement. This means there are no atomic coordinates saved in the PDBML-noatom files. The XML schema for the PDBML-noatom file is the same as the PDBML file provided at ... |
Get the chain IDs (auth_asym_ids and lable_asym_ids), entity IDs, entity names and type of chain (polymer or not) for PDB entiry 4uv7 - Search Services - PDBj Mine - SQL Search - Get the chain IDs (auth_asym_ids and lable_asym_ids), entity IDs, entity names and type of chain (polymer or not) for PDB entiry 4uv7 This search can be run from here. WITH t1 AS (SELECT DISTINCT e1.pdbid, ... |
[wwPDB] Improvements to visualization of ligand validation and electron density maps in the wwPDB validation report Our recent update to the wwPDB validation reports provides much clearer validation information for ligands. We now include 2-dimensional diagrams of ligands, highlighting geometric validation criteria and, for structures determined by crystallography, ... |