2017-06-28 : 4898 EMDB map entries, 1652 PDB coordinate entries PDBe | RCSB    

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Please Participate: 3D Volume Segmentation Survey

EMDataBank Partner PDBe (EBI) and their collaborators at the Science & Technology Facilities Council in Daresbury are developing a web service as part of the BioMedBridges project 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 models. For example: 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, the community was asked 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.

The PDBe/STFC Biomedbridges team now requests your input on 3D volume segmentation, which in many cases will be a necessary step before volume matching. What tools do you use and in which context do you use these tools? Your answers will help inform 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. Please take the survey at: https://www.surveymonkey.com/s/3dseg.