WORKSHOP Unlocking low-resolution structural biology data

Co-chaired by Martyn Winn (STFC; Instruct), Ardan Patwardhan (EBI; ELIXIR), et al.

This workshop will be of interest to researchers applying multiple structural techniques to particular biological systems, and to informaticians interested in the technical aspects of dealing with complex experimental data.

Structural biology provides complex data items, such as the 3D volumes of cryoEM, and searches involve complex operations and potentially inconclusive scoring of hits. Despite these uncertainties, there is a growing mass of structural volume data providing insights on the biological functions of macromolecules and their complexes. The starting point of this workshop will be the work done in BioMedBridges to provide a new data bridge between Instruct and ELIXIR concerning structural volume data from electron cryo-microscopy (cryoEM) and how to store, compare and annotate individual volumes in the absence of atomic coordinates.

In the first part we will demonstrate the work done by BioMedBridges:

  • The volume database, currently containing over 1000 volumes (or “maps”)
  • Overview of the new PDBeShape webservice
  • Technical details of volume/shape matching, and the SMaSB software
  • Generation and use of difference maps to understand stoichiometric differences, and conformational heterogeneity

The second part will look at future directions, including:

  • Desired updates to the functionality of PDBeShape
  • Maintenance and expansion of the underlying volume database, and improved data links
  • Relevant structural biology plans in CORBEL, the next life science cluster project, and West-Life
  • Other data sources, e.g. SAXS
  • Integration of molecular volume data with cellular biology, e.g. electron and soft X-ray tomographies
  • Re-purposing of the method for other biological domains, e.g. shape matching of entities from other imaging techniques

There will be plenty of time for discussion, and contributions from attendees are welcome.