PDBeShape
Information on the structure of macromolecules is important for biology and medicine because the function of many important biological processes can be directly linked to macromolecular structure or changes therein. For example, structural information on how a drug is bound to a target may yield vital clues on how to optimize its structure to promote more efficient binding.
BioMedBridges has developed a web-based shape-matching service that enables the wealth of low-resolution volume data in the EMDB and PDB resources to be searched based on their shape, providing entirely new perspectives on the relationships between structures. Shape matching also enables automated segmentation (the identification of sub-regions) of low resolution structures and the annotation of the segmentations with biological identifiers and ontologies. This in turn enables more effective meta-data searching of the structural data.
As a first step, the shape-matching software SMaSB was completed in December 2014 and is available as a compressed tarball from the downloads page of the CCP-EM project. A web-based shape-matching service was launched in June 2015.
Further information
- Web-based shape-matching service: PDBeShape
- Shape-matching software at CCP-EM (download link)
- REPORT: 9.1 Final version of the shape-matching software
- REPORT: 9.2 Final version of the web based shape-matching service
- Lagerstedt, I., Moore, W. J., Patwardhan, A., Sanz-García, E., Best, C., Swedlow, J. R., Kleywegt, G. J. (2013) Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB.Journal of Structural Biology, Volume 184, Issue 2 (Open Access) doi:10.1016/j.jsb.2013.09.021
- Use case 'Integrating structural data'