9.3 - Final version of the web-service for segmentation and identification of components in volume data

We have developed a software pipeline, named SMaSB, to perform automated volume/shape matching. Together with a database of over 1000 volumes from the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB), the pipeline underpins the PDBeShape web service. Together, these tools are novel in providing access to volume data, which constitutes a growing class of structural biology data. Deliverable 9.3 implements automated and manual segmentation into the PDBeShape web service. Automated segmentation with Chimera-Segger is now an integral part of volume pre-processing, with the results output as Chimera-Segger .seg files. Automated segmentation is useful as a guide to features in a volume, but does not reliably give segments corresponding to biological components (such as protein or RNA chains). Therefore, PDBeShape also supports annotation with the results of manual segmentation. As a proof of principle, 86 entries from the PDBeShape volume database were manually segmented and annotated, and the results are available from the PDBeShape service. Biological annotation links volume segments to entries in Pfam / Rfam and Uniprot.