Collaborative Computational Project
for Electron cryo-Microscopy


Computation for Biomolecular Cryo-Electron Microscopy and Tomography

July 13-14th 2017| University of Leeds

CCP-EM, CCPBioSim & University of Leeds are hosting two workshops on the theme of combining biomolecular EM and MD techniques.

Friday July 14th | Combining EM & MD Workshop

Structural characterisation of proteins and protein complexes with by cryo-EM and cryo-ET is now providing access to a wide range of macromolecular assemblies that were inaccessible by X-ray crystallography or NMR. Although EM analysis can provide information on different conformational states, it is still an averaging technique and therefore highly dynamic regions can be difficult to resolve. However, the image processing and interpretation of data from these experiments requires sophisticated computational hardware and software. This workshop will explore the emerging computational techniques for achieving biological understanding from cryo-EM/ET images, and discuss areas most in need of further development.

Sarah Harris, University of Leeds & Tom Burnley, CCP-EM / STFC
Setting the scene, what are the computational challenges for EM/ET? What can we do with simulation, and what else is needed?

Remy Martin (Berger-Schaffitzel Group), Univeristy of Bristol
An integrated approach to the structure and dynamics of the bacterial holo-translocon

Christian Blau (Lindahl Group), Stockholm University
Bayes' model for the ensemble behind cryo-EM densities

Max Bonomi (Vendruscolo Group), Univeristy of Cambridge
Simultaneous determination of protein structure and dynamics using cryo-electron microscopy

Jose-Maria Carazo, National Center for Biotechnology, Spain
Validation and quality control all way through from maps to models

Tristan Croll, University of Cambridge
Interactive MD for model building and validation

Agnel Joseph (Topf Group), Birkbeck
Refinement of atomic models in cryo-EM density using Flex-EM and assessment of fits with TEMPy

Elena Orlova, Birkbeck
Cryo EM or X-ray? Challenges, Achievements, and Prospects

Full schedule

Thursday 13th July | FFEA Practical Workshop

A hands-on workshop on the new software tool Fluctuating Finite Element Analysis (FFEA), which calculates dynamic trajectories for flexible biomolecules directly from cryo-EM/ET density maps. FFEA aims to provide an equivalent simulation tool for the EMDB as atomistic MD simulations have for the PDB. This approach uniquely, so uses volumetric meshes rather than atomistic co-ordinates as input such that it can model protein dynamics, protein-protein interactions, conformational switching between known configurational states and can be mapped back to atomistic co-ordinates, where these are available. This workshop is ideal for biomolecular simulators who would like to make full use of cryo-EM data in their modelling, or for experimentalists who would like to gain new theoretical insight into the dynamic behaviour of the structures they observe.

FFEA tutors: Sarah Harris, Albert Solernou, Daniel Read & Oliver Harlen (University of Leeds)

Full schedule


The Astbury Centre for Structural Molecular Biology, University of Leeds, UK


Directions to the University of Leeds campus


Delegates are asked to arrange their own accomodation has required. Suggested sites:

The Met Hotel, Leeds

Premier Inn, Leeds City Centre

Hotel Ibis, Leeds Centre


Registration is now open for both events:

Combining EM & MD Workshop

FFEA practical workshop