STRUCTURE VALIDATION USING F's
Tom Taylor & T. Alwyn Jones
Dept. Molecular Biology Uppsala University BMC BOX 590 S-751 24 Uppsala Sweden
A model deposited at the PDB is an interpretation of the experimental data. Validation methods exist to assess the quality of models based on stereochemistry and database knowledge [1,2]. These methods, however, are based purely on the model and ignore the experimental observations upon which the model is based. We are currently developing methods to facilitate the use of deposited structure factor information to supplement current validation tools. In addition, it is our intention to build a derived database where validation criteria and electron density based on deposited data will be available. Extensive use of VRML is being made as a WWW-friendly graphical interface for our results.
The first aspect of the work, which will be invisible to the user, is to generate routines to automatically interpret deposited files and to generate data for input into map calculation and refinement software. Once maps are generated, information relating the model to the map is generated, for example real-space R factors for each residue. In order to minimise the effect of model bias as much as possible, cross-validated SigmaA-weighted maps will be used.
Using the data generated in this manner, a set of WWW pages will allow the user to quickly and easily generate plots and view the information. In addition, an electron density server will be available for the inspection of the model with the corresponding map. By using these services, it will be possible for users of the structural database to pinpoint regions of the model which are poorly defined or partially disordered, regions which are not always obvious using stereochemical criteria alone.