2021 Ligand Model Challenge

last update: September 30, 2020

Goals

Identify metrics most suitable for evaluating and comparing fit of atomic coordinate models into cryo-EM maps for specimens in the <4.0 Å reported overall resolution range.

Specific focus areas:

1. Small molecules including ligands, water, metal ions, detergent, lipid, nanodiscs -- geometry and fit to map
2. Model geometry (including Rama, rotamers, clashes, EMringer, CaBLAM) in the neighborhood surrounding the small molecules
3. Local fit of model into map density per residue and per atom
4. Resolvability at residue or atom-level
5. Atomic Displacement parameters (B-factors) recommended optimization practice

Questions: How reliable are ligands built into cryoEM maps at X resolution? Can ligand be placed automatically or is manual intervention needed?

Committee

• Members: Paul Emsley, Andrej Joachimiak, Randy Read, Jane Richardson, Alexis Rohou, Bohdan Schneider, Jiri Cerny,  + the EMDR team.
  
• Charge: finalize targets, set guidelines for submissions, recommend evaluation procedures to include in our automated Challenge pipeline, and guide evaluation of results.

Timeline

• September 2020: Committee meets virtually to finalize targets, set guidelines for submissions, recommend evaluation procedures

Proposed Targets

The EMDR team recently reviewed over 70 recently determined cryo-EM structures containing drug-like compounds and selected those listed below as potential Challenge targets based on topical relevance and resolution range 2-3 Å.  These were reviewed at the initial Committee Discussion on Sept. 11, where the following were prioritized:

• 50S part of E. coli 70S ribosome
• SARS-CoV-2 Polymerase/remdesivir
• E. coli Beta-galactosidase: If possible have multiple maps at different resolutions for comparative analyses