Worldwide Protein Data Bank Policy Statement Governing Integrative/Hybrid Methods Structure Depositions

Preamble: The Worldwide Protein Data Bank (wwPDB) Partnership is committed to encouraging development of methods for archiving and validating structural data coming from Integrative/Hybrid Methods (I/HM).

The following policy governs wwPDB responses to requests from Depositors seeking to contribute I/HM structural data to the Protein Data Bank (PDB) archive.

Scenario 1: For I/HM atomic structures substantially underpinned by one or more experimental method currently supported by the PDB archive (NMR, 3DEM, or crystallography/diffraction) with some additional data provided by currently unsupported methods, the wwPDB will accept deposition of the atomic coordinates and supporting data (with a caveat explaining that the PDB archive was unable to store all of the data used to determine the I/HM structure) and strongly urge deposition of additional experimental data to existing data resources (e.g., SASBDB) where appropriate, and in the absence of an existing archival resource, to deposit the spatial restraints derived from other experimental and/or analytic methods to the PDB-IHM system (https://pdb-ihm.org).

Scenario 2: For I/HM atomic structures with no data coming from an experimental method currently supported by the PDB archive (NMR, 3DEM, or crystallography/diffraction) and all data coming from currently unsupported methods, the wwPDB will decline the deposition and strongly urge deposition of the atomic coordinates to the PDB-IHM system and deposition of experimental data to existing data archives where appropriate and in the absence of an existing archival resource, to deposit other spatial restraints used to compute the I/HM structure to the PDB-IHM system together with the atomic coordinates.

Scenario 3: For I/HM atomic structures only partially underpinned by an experimental method currently supported by the PDB archive (NMR, 3DEM, or crystallography/diffraction) with the majority of the data coming from currently unsupported methods, a decision will be made on a case by case basis to either

1. Accept deposition of the atomic coordinates and supporting data (with a caveat explaining that the PDB archive was unable to store all of the data used to determine the I/HM structure) and strongly urging deposition of the additional experimental data to existing data archives where appropriate, and in the absence of an existing archival resource deposit other spatial restraints used to compute the I/HM structure to the PDB-IHM system;
   Or
   
2. Decline deposition of the atomic coordinates and supporting data and strongly urge deposition of the atomic coordinates using the PDB-IHM system and deposition of experimental data to existing data archives where appropriate, and in the absence of an existing archival resource deposit the other spatial restraints used to compute the I/HM structure to the PDB-IHM system together with the atomic coordinates.

Scenario 4: For partially or entirely non-atomic I/HM structures, the wwPDB will decline the deposition and strongly urge deposition of the coordinates and experimental data to existing data archives where appropriate, and in the absence of an existing archival resource to deposit experimental data, other spatial restraints used to compute the I/HM structure to the PDB-IHM system together with the coordinates.