Dear Colleagues, PDBe 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 on 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 in the archives. We will also use the service to automatically fit and segment existing entries when new entries are deposited that share common components, e.g. a newly deposited ribosomal protein will be fitted into ribosomal maps in the PDB/EMDB and 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.
We are taken our first baby steps in this project and need your help to avoid reinventing the wheel - we want to use existing software wherever possible! We would like to know what tools and in which context you use fitting software, including fitting atomic coordinates in a volume, fitting EM single particle volumes in tomograms, comparing an EM volume with a SAXS envelope, and comparing a EM single particle volume with a sub-tomogram average. Please take a moment to fill in our questionnaire on shape/volume fitting in structural biology following this link http://www.surveymonkey.com/s/BioMedBridgesShapeMatchingSurvey to Survey Monkey. We plan to publish an anonymized summary of the survey on the BioMedBridges web site. Kind Regards, Ingvar Lagerstedt & Ardan Patwardhan, PDBe and Martyn Winn, STFC * * Dr. Martyn Winn * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * Tel: +44 1925 603455 (DL) or +44 1235 567865 (RcaH) * E-mail: martyn.w...@stfc.ac.uk Skype: martyn.winn * -- Scanned by iCritical.
