We has frozen the PDBMLplus on PDBj FTP site. As announced previously, PDBMLplus files provided from PDBj ftp site has been frozen on 9 July, and will not be updated. Alternatively, you can use the interface in PDBj Mine, which generates it on demand from now on as follows; - Merged on demand for ... |
News on 2014-7-9 Large Structures has been released" /> Improved Representation of Large Structures in the PDB Archive (wwPDB News) |
PDB Reaches a New Milestone: 100,000+ Entries ( wwPDB News ) PDB Reaches a New Milestone: 100,000+ Entries (wwPDB News) |
The Road to 100,000 Entries: Launching Tools for the Next Generation ( wwPDB News ) The Road to 100,000 Entries: Launching Tools for the Next Generation (wwPDB News) |
The Road to 100,000 Entries: The Early Structures ( wwPDB News ) The Road to 100,000 Entries: The Early Structures (wwPDB News) |
The Road to 100,000 Entries: Building a Community Resource ( wwPDB News ) The Road to 100,000 Entries: Building a Community Resource (wwPDB News) |
We'll finish to provide the PDBMLplus from FTP site. The default URL of PDBMLplus was changed in jV version 4.4 for this change. We'll finish to provide the PDBMLplus from FTP site We are providing the PDBMLplus, which is created by adding extra information collected by PDBj into PDBML-noatom (canonical PDB data file with XML format without atom coordinates), in following two ... |
The jV 4.4 was released. As the default URL of PDBMLplus file was changed. So we recommend for all jV users to update jV to this version. The jV 4.4 was released We announce the new version of jV (jV 4.4) was released. In this version, load/save function of mmCIF format file and biological unit was implemented. And the default URL of PDBMLplus file was changed. So we recommend for all jV ... |
A fasta file for all the sequence information is now available from the PDBj ftp site. In addition to fasta sequence information ('fasta_seq_data/PDBID_seq.txt') for each PDB entry, a fasta file for all the sequence information ('all_fasta_sequence.txt.gz') is now available from the PDBj ftp site. |
wwPDB X-ray validation reports added to PDB archive ( wwPDB News ) wwPDB X-ray validation reports added to PDB archive (wwPDB News) |
Mine2 RDB (Mine 2 Relational DataBase) was released from FTP site on Wednesday, March 5, 2014. For more details, please refer to the help page . Mine2 RDB (Mine 2 Relational DataBase) was released from FTP site on Wednesday, March 5, 2014. For more details, please refer to the help page. |
Archiving Structures Derived from SAS Data ( wwPDB News ) Archiving Structures Derived from SAS Data (wwPDB News) |
New wwPDB Deposition System Now Available for X-ray Structures ( wwPDB News ) New wwPDB Deposition System Now Available for X-ray Structures (wwPDB News) |
Coming soon: X-ray Validation Reports for Archived PDB Structures ( wwPDB News ) Coming soon: X-ray Validation Reports for Archived PDB Structures (wwPDB News) |
wwPDB Partners Prepare to Launch New Deposition System ( wwPDB News ) wwPDB Partners Prepare to Launch New Deposition System (wwPDB News) |
Announcement: Standardization of Amino Acid Nomenclature ( wwPDB News ) Announcement: Standardization of Amino Acid Nomenclature (wwPDB News) |
Download the wwPDB calendar for IYCr:2014 ( wwPDB News ) Download the wwPDB calendar for IYCr:2014 (wwPDB News) |
PDBx/mmCIF Resources The wwPDB is going to start to use a new standard format, PDBx/mmCIF in 2014, replacing the legacy "PDB format" that has been used since nineteen-seventies. The details are shown in the Web page for the new standard format. |
The 12th AsCA will be held in Hong Kong from 7 to 10 December. Haruki Nakamura, Head of PDBj will give a poster presentation to introduce PDBj's web services and our latest activities. The following seminar was finished. The 12th Conference of the Asian Crystallographic Association The 12th AsCA will be held in Hong Kong from 7 to 10 December. Genji Kurisu will give an oral presentation about "Modifications to the Protein Data Bank ( ... |
PDBj Mine:XPath - XPath - Examples - Search for PDB ID (1GOF): Search for Revision information for a pdbid named 1gof: Search for entity_poly data with polypeptide(L) chain type: Search for entity data with EC number 1.1.1.1: Search for PDB title data: Search for PDB ... |
The wwPDB is going to start to use a new standard format, PDBx/mmCIF in 2014, replacing the legacy \ The wwPDB is going to start to use a new standard format, PDBx/mmCIF in 2014, replacing the legacy "PDB format" that has been used since nineteen-seventies. The details are shown in the Web page for the new standard format. |
New wwPDB service allows crystallographers to validate their own structures ( wwPDB News ) New wwPDB service allows crystallographers to validate their own structures (wwPDB News) |
NER COLOR The NER score is evaluated on a per-residue basis, and expressed as an integer from 0 (worst) to 9 (best). The following color scale is used to represent each integer value: 0 1 2 3 4 5 6 7 8 9 |
The end of Distribution of uncompressed PDBMLplus files Distribution of uncompressed PDBMLplus files will end on December 31, 2013. Please use the compressed (gzipped) version instead. |
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