PSI Structural Biology Knowledgebase

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Policy on using PSI Structures for a Rolling Critical Assessment of Modeling and Experimental - Computational Hybrid Methods

The policy of the PSI is to deposit to the PDB and BioMagResDB, for immediate release, the coordinates and supporting diffraction and/or NMR data of protein structures as soon as they are completed.

It is, however, recognized that certain technology development projects can benefit from “blind test” cases. These include methods for protein structure prediction, as well as hybrid methods using sparse experimental data together with computational methods.

In order to facilitate such methods development, the PSI will allow a limited number of structures (10 – 12 per center, per year) to be deposited into the PDB with 8-week hold times. In addition, certain data (e.g. NMR chemical shift data or limited numbers of experimental constraints) for these structures will be made freely available on the public web sites of the corresponding PSI centers.

It is the aim of this program to nurture and support development, by the broader scientific community, of new methods of protein structure determination without compromising key objectives of the PSI, which include rapid, unrestricted release of structural data.

In creating these data sets, PSI depositors will select the “8-week hold” option, and then manually add the key word “Methods Development” during their structure deposition. This will be the way in which these special structures are recognized and will be handled accordingly by the PDB annotation staff. Atomic coordinates for these structures will be made available from the Centers, prior to the 8-week release, upon request.

The corresponding PSI Center is responsible to publicize, on their respective public web sites, the availability of these data for methods development, including (i) the protein sequence; (ii) date of deposition of coordinates, (iii) anticipated date of release of coordinates and supporting experimental data, (iv) partial experimental data useful for new technology development. A list of proteins for which such experimental data is available and a link to the center and center contact will be posted on the PSI KB Nature Gateway site.

1/7/2008

Structural Biology Knowledgebase ISSN: 1758-1338
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