PDBe (EBI) and STFC are developing a web service as part of the BioMedBridges project (http://www.biomedbridges.eu/workpackages/wp9) that will enable the EMDB and PDB archives to be searched on the basis of 3D volumetric shape matching, rather than solely on the basis of metadata and/or coordinate model.
- users will be able to upload a 50S ribosome map and retrieve aligned maps of other ribosomes from the archives
- when new entries are deposited, the service will automatically fit and segment existing entries that share common components, e.g. a newly deposited ribosomal protein will be fitted into ribosomal maps in the PDB/EMDB. The resulting segmentations will be made publicly available.
In due course, the service may be extended to other volumetric data, such as from SAXS or soft X-ray tomography.
In February-March 2013, we asked the community for input on shape/volume matching. The questions covered protocols followed, usage issues, as well as specific software. A report on the findings can be viewed at http://www.biomedbridges.eu/biomedbridges-wp9-shape-matching-survey
We now wish to consult the community regarding volume segmentation, which in many cases will be a necessary step before volume matching. We would like to know what tools you use and in which context you use these tools. Your answers will help inform our development, and ensure the service meets the needs of the community. While the proposed service is most relevant to structural biologists, segmentation is a widely used technique, and input from other communities would be very useful.
Ingvar Lagerstedt & Ardan Patwardhan, PDBe (EBI) and Agnel Praveen Joseph & Martyn Winn, STFC