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... all new X-ray crystal structures deposited PDBe, PDBj, and RCSB PDB as of August 1, 2013. "Validation 'at the gate' is ... validation reports for all X-ray crystal structures already in the PDB archive will be made publicly available as PDF files, together ...

... wwPDB biocurator Dr. Brian Hudson on processing over 10,000 PDB depositions! Dr. Hudson received his PhD in Chemistry from the ... X-ray crystallography and cryo-electron microscopy. He has joined PDB in 2010 and has established himself as a highly qualified ...

... 3.15 to be Released A new standardized version of the PDB archive will be available from ftp://ftp.protein.osaka-u.ac. ... released prior to December 2, 2008 will be re-released as PDB Format Version 3.15 files. This release will overwrite all existing ...

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EM Data Bank joins the PDB archive The EM Data Bank (EMDB) has joined the PDB archive on March 7, 2012. Now it is available from PDBj ftp site at ftp://pdb.protein.osaka-u.ac.jp/pub/emdb. ( wwPDB News... )

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... via rsync is started. We have started to provide remediated PDB archive via rsync protocol. Rsync is a software which synchronizes files ... transfer using delta encoding when appropriate. Detailed information for PDB archive service is available from ...

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... wwPDB/RDF. PDBj has been providing RDF(Resource Description Framework)-formatted PDB data based on the pdbj.org domain. From now on, ... change. - http://pdbj.org/rdf/1GOF -> http://rdf.wwpdb.org/pdb/1GOF - http://pdbj.org/chem_comp/ATP -> http://rdf.wwpdb. ...

... her PhD in Environmental Engineering from Osaka University and joined PDB after working at the National Cerebral and Cardiovascular Center, ... Osaka. She has joined PDB in 2007 and is now working at the branch ...

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... access to integrated annotations and enriched structural information for PDB data: NextGen Archive: Centralising Access to Integrated ... provided in the structure model files in the PDB main archive. The inclusion of UniProtKB numbering facilitates ...

... . import urllib, json url = "https://pdbj.org/rest/newweb/search/pdb" params = "rdate_after=2014-01-01&method=1&res_max=1 ... the exact same query for the Related PDB entries tab. The script searches for all related PDB entries for a given chem_comp id ...

... model. The fitting service between two EMDB density maps or PDB structures is available through the WEB. URL: http://pdbj. ... HOMCOS is a service for searching 3D complex structures in PDB from sequences or chemical structures, and for modeling 3D complex ...

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... Protein Research, Osaka University) "Modifications to the Protein Data Bank (PDB)" - Date&Time: Sunday 8 December 10:50-11:15 ... , Osaka University) - "Modifications to the Protein Data Bank (PDB)" - Poster Presentation Date&Time: Monday 9 December 16:15-18 ...

... At the time the structure was solved, there were no PDB entries with significant sequence homology, however conservation and geometry of ... pathway. Currently, the closest match to 1uan in the PDB is 2ixd, a putative deacetylase from Bacillus cereus that was ...

... data (v4.0). Please download the newest version from here. PDB Archive Version 4.0 has been released on July 13, 2011. ... wwPDB has released the new version of the PDB data, which reflects the review and resulting changes and corrections. ...

... easily reviewed and shared by depositors. As these PDB validation reports provide an assessment of structure quality ... further develop our data deposition and processing procedures. PDB validation reports are already required by the International Union ...

... .org/pdbjplus/data/cc/mmjson-plus/ and at each individual PDB entry page. - The sequence navigator/neighbor interface has been ... functionality has been moved from the server-side using legacy PDB flat files to the client-side with Molmil using mmJSON files ...

... metadata, the RDB Query Builder enables more flexible filtering of PDB/chem_comp/BIRD/EMDB entries using all the metadata included ... options show the results similar to the quick search for PDB, Chemie and BIRD. The available options depend on the search ...