Next Generation of ADIT and ADIT-NMR Available for Depositions and Testing

When depositing your next structure, try using either beta-ADIT or beta-ADIT-NMR.

Beta-ADIT (http://deposit-beta.rcsb.org/adit/)has been designed to make your deposited entries more complete and error-free. This tool offers a number of advantages over the current version of ADIT, including:

Consistency checking between sequence and coordinates
Indication of format errors, with suggestions for solutions
Easier options for entering author information

Structures deposited using beta-ADIT will result in real deposition sessions that will be processed by annotators. beta-ADIT will become the only version of ADIT after a period of testing. Please help us improve this tool by sending your feedback to deposit@deposit.rcsb.org.

Beta-ADIT-NMR (http://batfish.bmrb.wisc.edu/bmrb-adit/) can be used to create individual or combined NMR depositions to the BMRB and PDB archives.

This new deposition system accepts multiple NMR data files – structural (e.g., coordinates) and experimental (e.g., constraints, chemical shifts, coupling constants, relaxation data, pKa). The RCSB PDB and BMRB have developed this single tool so that depositors would not be required to use two different tools to deposit these data.

Once data is deposited using beta-ADIT-NMR, they will be processed (structural data at the RCSB PDB, experimental data at the BMRB), and be available for download at their respective public domains.

Questions and suggestions about beta-ADIT-NMR should be sent to bmrbhelp@bmrb.wisc.edu.

RCSB 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 process simpler:

Structures solved using X-ray crystallography or NMR should be prepared using pdb_extract before using ADIT. This will minimize manual typing and save time during the deposition process. 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 included in a text file that is prepared once and used for running 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 deposit@deposit.rcsb.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 your 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 the entries they are associated to expedite the processing of these files.

The Searchable PDB Exchange Dictionary

The information collected, processed and distributed by the wwPDB is all defined in the PDB Exchange Dictionary.(1) This dictionary, along with several other dictionaries, can be searched using the text box at the top of the Dictionary Resources page, and browsed using the HTML version. The XML Schema for the PDB Exchange Data Dictionary is also available for download.

http://mmcif.pdb.org contains a variety of Dictionary Resources

The PDB Exchange Dictionary includes definitions for X-ray crystallography, NMR, 3D EM, and protein production. These definitions were developed and reviewed by discipline experts and by the member organizations of the wwPDB.

There are currently 3395 definitions in the PDB Exchange Dictionary that are divided into 283 categories. The categories are organized into groups of related definitions analogous to the organization of related columns in a table.

The search form available for data dictionaries at http://mmcif.pdb.org. To search for a particular item, select the dictionary you want to search from the pulldown menu, enter the term in the box provided, and select "go".

The PDB Exchange Dictionary uses the dictionary language developed for the macromolecular Crystallographic Information File (mmCIF) dictionary (2). The dictionary includes textual definitions and examples as would be found in any language dictionary, as well as data type, boundary conditions and controlled vocabularies that can be used by software applications to validate and maintain uniformity of usage in data files. Since the dictionary is fully software accessible it can also be translated into alternative formats, as has been done in the case of the eXtensible Markup Language (XML) to provide a PDBML dictionary.(3)

Questions and comments should be sent to info@rcsb.org.

Westbrook, J., Henrick, K., Ulrich, E.L. and Berman, H.M. (2005) In Hall, S. R. and McMahon, B. (eds.), International Tables for Crystallography. Springer, Dordrecht, The Netherlands, Vol. G. Definition and exchange of crystallographic data, pp. 195-198.
Fitzgerald, P.M.D., Westbrook, J.D., Bourne, P.E., McMahon, B., Watenpaugh, K.D. and Berman, H.M. (2005) In Hall, S. R. and McMahon, B. (eds.), International Tables for Crystallography. Springer, Dordrecht, The Netherlands, Vol. G. Definition and exchange of crystallographic data, pp. 295-443.
Westbrook, J., Ito, N., Nakamura, H., Henrick, K. and Berman, H.M. (2005) PDBML: The representation of archival macromolecular structure data in XML. Bioinformatics, 21, 988-992.

2006 Deposition Statistics

As of October 1, 5376 structures have been deposited to the PDB this year.

The entries were processed by the wwPDB teams at RCSB PDB, MSD-EBI, and PDBj. Of the structures deposited, 69.3% were deposited with a release status of "hold until publication"; 17.8% were released as soon as annotation of the entry was complete; and 12.9% were held until a particular date.

81.9% of these entries were determined by X-ray crystallographic methods; 12.5% were determined by NMR methods; and 82.6% of all of these depositions were deposited with experimental data.