Validate Before Depositing to Save Time


During annotation of X-ray crystallographic entries, wwPDB provides depositors with reports that include the results of model and experimental data validation. Depositors then have the option to make changes and corrections to their submission, which can cause delays in the final submission, review, and release of the entry.

The standalone validation server for X-ray crystallographic entries at lets experimental structural biologists validate structural models prior to publication and deposition.  The reports created with this server can be used to make the corrections and changes to data files needed before starting the deposition process.

Validating data before deposition helps to ensure the most rapid and efficient submission and processing of data.

wwPDB Validation Reports were developed according to the recommendations of the wwPDB X-ray Validation Task Force (1,2). Several programs, including MolProbity, Xtriage, Mogul, EDS and various CCP4 programs, are used to generate the results of geometry checks, structure factor validation, and ligand validation.

Validation options for NMR and EM structures will be made available at a later date.

(1) Read RJ, Adams PD, Arendall WB, III, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lutteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH. (2011) A new generation of crystallographic validation tools for the Protein Data Bank. Structure 19: 1395-1412. doi: 10.1016/j.str.2011.08.006

(2) Gore S., Velankar S. and Kleywegt G.J. Implementing an X-ray validation pipeline for the Protein Data Bank 2012, Acta Cryst., D68, 478-483. doi: 10.1107/S0907444911050359

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