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2020 Ligand Model Challenge

last update: September 11, 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

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

• Late September: Announce the Challenge, enable registration
• Early December: Submissions close
• Early February: Initial evaluation results ready for review
• Early March:  Committee meets to discuss evaluation results, make plan for final report.
 

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.

 

Priorities based on Discussion Sept. 11:

  • 50S part of 70S ribosome (as long as it is deposited in PDB/EMDB)
  • SARS-CoV-2 Polymerase/remdesivir
  • Beta-galactosidase
  • If possible have multiple maps at different resolutions for comparative analyses

 

Specimen

IDs

Ligand

Resol (Å)

notes

E. coli β-Galactosidase

EMD-10574 | 6tte

PETG (enzyme inhibitor)

2.2

half-maps are available

SARS-CoV-2 RNA-dependent RNA polymerase

EMD-30210 | 7bv2

Remdesivir (covalent inhibitor)

2.5

half-maps requested, positive response

 

 Additional Suggestions:

EMDataResource Validation Challenges are supported by NIH National Institute of General Medical Sciences

Please send your challenge questions, comments and feedback to challenges@emdataresource.org

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