Tour of Ligand Deposition


wwPDB launched the Deposition Tool for structures determined using X-ray crystallography on January 27, 2014 as part of a new Deposition and Annotation System. Since then, more than 10,200 structures have been deposited and annotated, and more than 5,600 structures released in the archive using this system.

Videos demonstrate how to review and submit ligands with the wwPDB Deposition Tool.

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:

The wwPDB Deposition Tool is used for X-ray crystallographic data; similar tools for NMR and 3DEM will be available in 2016.  Up-to-date information about the Deposition Tool, tutorials for getting started, and an FAQ are available from the wwPDB website.

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