PDB Focus: Releasing HOLD and HPUB structures
Structure data can be held for a maximum period of one year between the deposition and release of any entry, even if the paper associated with an HPUB structure is still unpublished.
Data can always be released before the paper is published. The citation information can then be updated at a later date.
When a structure has been on hold for a year, we ask the author to release or withdraw the structure. Withdrawn entries can be redeposited at a later time, at which point a new PDB ID will be issued.
We try to release HPUB files as close to the publication date as possible. The PDB receives publication dates and citation information from some journals. For other journals, the PDB scans the literature for publication information (using the deposited author names and deposited article title). We also greatly appreciate having citation information sent to email@example.com.
PDB Focus: Tips for depositing multiple related structures using ADIT
When depositing many structures that are related to one another, there are a few ways of making the ADIT deposition process simpler:
- Structures solved using X-ray crystallography should be prepared using pdb_extract before using ADIT. This will minimize manual typing and save time during deposition. pdb_extract takes information about data collection, phasing, density modification, and the final structure refinement from the output files and log files produced by the various applications used for structure determination. The collected information is organized into a file ready for deposition using ADIT. Information duplicated in all entries (author name, citation information, protein names, etc.) can be compiled into a single text file to run with pdb_extract for each entry. After pdb_extract has combined all the available information into a single file for each structure, ADIT can be used for quick deposition.
- A similar tool is being developed for structures solved by other experimental methods. For these structures, deposit one representative structure following the instructions provided at deposit.pdb.org. Then write to firstname.lastname@example.org to let us know about the other related entries. Once the first entry has been annotated, processed and finalized, it can be used as a template for subsequent depositions. For each structure, replace the coordinates and update the information in the header section of the PDB file as necessary to prepare the related files for deposition.
- If the structures have ligands, drugs or inhibitors bound to them, please check Ligand Depot and match the 3 letter code in the file to the one used in the chemical component dictionary. If the ligand is not present in the dictionary, please email detailed information (complete chemical name, 2D figure showing connectivity, bond order and sterochemistry) along with the RCSB and PDB IDs of associated entries to expedite the processing of these files.
PDB DEPOSITION STATISTICS
4894 experimentally-determined structures have been deposited to the PDB archives as of October 1, this year.
The entries were processed by wwPDB team members at RCSB, MSD-EBI, and PDBj. Of the structures deposited, 69% were deposited with a release status of HPUB; 17% with REL; and 14% with HOLD.
81% of these entries were determined by X-ray crystallography; 16% were determined by NMR. 81% were deposited with experimental data. 56% released the sequence in advance of the structure's release.