Collaborative Computational Project
for Electron cryo-Microscopy


Cryo-EM Validation in the Age of SARS-CoV-2: Methods, Tools and Applications

Useful links


Discord server


18, 19 & 20 November 2020 | Online

As the UK EM Validation Network, we have organised this meeting to present current thinking on cryo-EM map and map/model validation, and to consider future research directions that anticipate the growing needs in this area. The community effort to apply cryo-EM to structural proteins of SARS-CoV-2 has been a success story but has also highlighted the importance of structure validation.

Each day will consist of two sessions with talks and a panel discussion, with the following themes:

Day 1: 18th Nov Analysis and validation of SARS-CoV-2 EM structures
Day 2: 19th Nov Single particle map and tomogram validation
Day 3: 20th Nov Map-model validation

The meeting organisers are supported by a technology-development grant from the Wellcome Trust. An earlier (in-person) workshop held in January 2019 at EMBL-EBI was a great success and we expect the November meeting to be equally interesting and to reach a considerably larger audience through the online format.

Scientific organisers:

© Goodsell et al. 2020

Gerard Kleywegt (EMBL-EBI)
Garib Murshudov (MRC-LMB)
Elena Orlova (Birkbeck College)
Ardan Patwardhan (EMBL-EBI)
Alan Roseman (University of Manchester)
Peter B. Rosenthal (The Francis Crick Institute)
Maya Topf (Birkbeck College)
Martyn Winn (STFC)

Registration website

Please register in advance of the meeting here. Registration is free of charge, but is required for attendance.

How it will work

The main sessions and panel discussions will take place via Zoom. A link to join will be sent to you before the meeting. This link is personal to you, and you will need it to access the talks on Zoom.

We have also set up a Discord server for the meeting. Click here to access. Discord is a platform for text and video discussions which is very popular in the gaming community. For this meeting, the server will enable discussions to continue outside the Zoom sessions. We will support general discussions, as well as channels for ad hoc groups of people.


Note that all times are in UK local time (GMT). A full schedule is available for download.

Wednesday 18th November - Analysis and validation of SARS-CoV-2 EM structures

  • 14:00 - 15:30 Session 1 (Chair: Peter Rosenthal)
  • 14:00 Peter Rosenthal (Crick) "Welcome and logistics"
  • 14:10 Ardan Patwardhan (EMBL-EBI) "SARS-CoV-2 structures in EMDB and EMPIAR"
  • 14:30 Patrick Cramer (MPI Göttingen) "Structural studies of SARS-CoV-2 polymerase and mechanism of remdesivir inhibition"
  • 14:50 Christiane Schaffitzel (Bristol) "A free fatty acid binding pocket in the locked structure of SARS-CoV-2 spike protein"
  • 15:10 Beata Turoňová (EMBL) "In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges"
  • 15:45 - 17:00 Session 2 (Chair: Garib Murshudov)
  • 15:45 Donald Benton (Crick) "Structural basis of SARS-CoV-2 Receptor Binding"
  • 16:05 Andrea Thorn (Hamburg) "Findings from the Coronavirus Structural Task Force"
  • 16:25 Tristan Croll (Cambridge) "Rebuilding SARS-CoV-2 Cryo-EM structures with ISOLDE"
  • 16:45 Agnel Joseph (STFC) "Reprocessing and validation of structures from SARS-CoV-2 and a web service for mapping genome mutations"
  • 17:30 - 18:00 Panel discussion (Moderator: Peter Rosenthal)

Thursday 19th November - Single particle map and tomogram validation

  • 14:00 - 15:20 Session 3 (Chair: Ardan Patwardhan)
  • 14:00 Carsten Sachse (Jülich)"Significance and confidence of cryo-maps and resolution values"
  • 14:20 Sjors Scheres (MRC-LMB Cambridge) "Single-particle cryo-EM to atomic resolution"
  • 14:40 Dmitry Lyumkis (Salk) "Tools for Analyzing Directional Resolution and Fourier Space Sampling in Cryo-EM"
  • 15:00 Tim Grant (UW-Madison) "Preventing overfitting in cisTEM by local SNR weighting"
  • 15:35 - 17:00 Session 4 (Chair: Alan Roseman)
  • 15:35 Katerina Naydenova (MRC-LMB Cambridge) "Specimen supports for high-resolution cryoEM: application for determining the structure of the SARS-CoV-2 RNA polymerase in presence of favipiravir"
  • 15:55 Niko Grigorieff (UMass Medical School) "Locating molecular assemblies by template matching in 2D and 3D: a comparison"
  • 16:15 Giulia Zanetti (Birkbeck) "Common issues in subtomogram averaging: my perspective on current needs and validation"
  • 16:30 Valeriy Titarenko (Manchester) "Global and local model fitting and scoring for cryo-EM maps"
  • 16:45 Lucas Siemons (Crick) "Applications of tilt-pair analysis"
  • 17:30 - 18:00 Panel discussion (Moderator: Elena Orlova)

Friday 20th November - Map-model validation