WP9 Use case: From cells to molecules - integrating structural data |
Survey of shape/volume fitting in structural biology
PDBe (EBI) and STFC are developing a web service as part of the BioMedBridges project (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 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.
We are taking 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 you use 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.
Many Thanks,
Ingvar Lagerstedt & Ardan Patwardhan, PDBe (EBI) and Martyn Winn, STFC
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.
We are taking 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 you use 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.
Many Thanks,
Ingvar Lagerstedt & Ardan Patwardhan, PDBe (EBI) and Martyn Winn, STFC