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Last update: 2013-3-01

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PDBj Validation & Deposition Portal

Welcome to the PDBj validation/deposition portal.

Need help?

If you have any questions, please read “Deposition tutorial” first. If you still need help, please contact us. Questions, comments, and suggestions in validation/deposition service and tutorial are welcome.


Data Deposition Tools

Search

You may search HET groups using Ligand Expo. If your HET groups are NOT new, you should use the existent ones.

Check sequence database references for proteins or nucleic acids in your structure at UniProtKB. The author is encouraged to submit their sequence information via SPIN (the UniProtKB submission tool) for directly sequenced proteins, or vir submission tools provided by INSDC members (SAKURA at DDBJ, Webin at EMBL, BankIt at GenBank) if the nucleotide sequence is available.

Validate

Before you deposit the structure data, validate your structure using the validation server at PDBj.

» ADIT validation logoADIT Validation Server

Deposit

After you validate your structure data, deposit your structure using the structure deposition tool ADIT at PDBj or ADIT-NMR at PDBj (for NMR studies). For other deposition servers at wwPDB member sites, please visit from the wwPDB web site.

» ADIT logoADIT

» ADIT-NMR logoADIT-NMR

For small peptide structures solved by NMR, you can use SMSDep at BMRB.

Structures solved by electron microscopy should have their maps deposited to either the EMDep at PDBe or RCSB first, permitting the user to supply the EMD-id as an associated entry with their ADIT deposition.

After the deposition...

After the deposition, you will receive an email receipt which includes PDB ID and RCSB ID.

wwPDB annotator will send the letter which includes validation summary, question about your entry, etc. to the contact authors. The authors need email communication with wwPDB annotator in English.


Policies and Procedures

Data Processing and Annotation Procedures Manual (updated December 2008)
Processing manual using at PDBj and RCSB.
PDB File Format Documentation
File format information for files which wwPDB provides.
wwPDB Annotation Documentation
wwPDB policies and Procedures document. Authors are encouraged to understand “Processing Procedures ” and “Annotation Policies” documents.
Theoretical Model Policy Statement
wwPDB policy statement fot theoretical model studies (Theoretical model depositions are not acceptable now).
PDB Data Release Policies
Policy document for data depositon and release. Please note that deadline for the release request in PDBj is 12:00 noon JST (Japan Standard Time) on the preceding Thursday.
Deposition tutorial in English, Japanese, Korean, Simplified Chinese, Traditional Chinese
You can see the tutorial in proper language which is set to your web browser. If you can't see tutorial in your prefered language, please setup your browser. See instruction on “How to set the default document language

News

2012-12-4
Effective February 6, 2013, coordinates and experimental data deposited in the PDB will follow the same release status. (wwPDB News...)

» Full News


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