Tour of Ligand Deposition


As announced by the wwPDB, a new deposition system for structures determined using X-ray crystallography has been launched. New or enhanced features of this system include the generation of X-ray validation reports (following the recommendations of the wwPDB X-ray Validation Task Force), improved capture and review of ligand information, the ability to replace coordinate and/or experimental data files pre- and post-submission, improved communication process between depositors and wwPDB curators, and the ability to preview and download the PDBx/mmCIF entry file prior to submission.

New videos demonstrate how to review and submit ligands in this new system.   

For all ligands present in the uploaded coordinate file, the deposition system will search for graphical matches against all released ligands in the PDB. Close (but not exact) matches will require depositor attention as demonstrated here:

When the system cannot find a match for a ligand, depositors will be required to provide a SMILES or InChI string or a 2D chemical drawing, as shown in this video:

Depositors will have the option to use the new system or one of the legacy deposition tools (ADIT, AutoDep) for most of 2014. After the transition to the new system, the legacy tools will be available for a limited period of time to complete any unfinished deposition sessions.

In the interest of a smooth transition, the number of X-ray structures that will be processed by the new system will increase gradually over the next few months. After this period, it will also become possible to deposit NMR and 3DEM structures with the new system.

Up-to-date information about the new system, tutorials for getting started, and an FAQ are available from the wwPDB website.

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