Biomedbridges: Final Fully Integrated Version Of Software To Estimate The Probability Of Various Conformations
Antonio Rosato, Martyn Winn · INFM-OAR (INFN Catania) · 2016
We have developed a software pipeline, named SMaSB, to perform automated volume/shape matching (Deliverable D9.1). Together with a database of over 1000 volumes from the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB), the pipeline underpins a web service PDBeShape (Deliverable 9.2). Deliverable 9.3 implemented automated and manual segmentation into the PDBeShape web service. A segment-level description of volume data allows a precise annotation of multi-component complexes, linking out to relevant bioinformatics resources. However, a given protein component, described by a single UniProt ID, may adopt different conformations in different complexes reflecting its particular function in each complex. The resolution of volume data does not always allow the precise conformation to be determined, although it may limit the possibilities. It is therefore appropriate to include a level of structural annotation. In this deliverable, we use an analysis technique developed for NMR and SAXS data to provide structural annotation for components in the PDBeShape volume database. The output is a set of conformations that a protein component can adopt, and that are consistent with the volume data. The approach utilises multiple data sources for structural biology. As more structural biology data is collected, the range of conformations that are possible can be narrowed, and the structural annotation updated.