[3dem] Questionnaire on shape/volume fitting in structural biology

[ingvar]

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