[3dem] Questionnaire on shape/volume fitting in structural biology
ingvar
ingvar at ebi.ac.uk
Thu Feb 28 07:58:32 PST 2013
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
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