Final Version Of The Web-Based Shape-Matching Service
Martyn Winn, Ardan Patwardhan, Agnel Praveen Joseph, Ingvar C. Lagerstedt · Zenodo (CERN European Organization for Nuclear Research) · 2015
A software pipeline, named SMaSB, was previously developed to perform the volume/shape matching that underpins the set of tools being developed in WP9. These tools are novel in providing access to a growing class of structural biology data viz. volume data. The SMaSB software is primarily a set of Python codes which organise the metadata, control the data flow during volume/shape matching, and record the results. Third-party software is called to perform the compute-intensive steps in the pipeline. The first full version of SMaSB was released in December 2014, and reported in Deliverable 9.1. We now report on the associated web service (PDBeShape) which provides a user-friendly front-end to SMaSB results. It provides web access to a curated database of structural volumes, derived from deposited structures in the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB), together with pre-processed alignments and scores. We have made the first version of the PDBeShape service publically available at http://wwwdev.ebi.ac.uk/pdbe/emdb/shape/welcome/. In this document, we give details on the current functionality of PDBeShape, and the technical underpinning. More extensive documentation is provided on the web page.