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2020 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

• 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.  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

 

Specimen EMDB ID PDB Reference Ligand Resol (Å) citation notes
E. coli β-Galactosidase(EMPIAR 10061 original and reprocessed)

EMD-2984

EMD-7770

EMD-8908

EMD-0153

6cvm

PETG (enzyme inhibitor

2.2-1.8

Bartesaghi2015

Subramaniam2018

Cianfrocco2018

Zivanov2018

half-maps are available
SARS-CoV-2 RNA-dependent RNA polymerase EMD-30210 7bv2 Remdesivir (covalent inhibitor) 2.5 Yin2020 half-maps requested
E. coli 70S Ribosome (intended focus: 50S) EMD-22586 7k00 Paramomycin 2.0 Watson2020 composite map, related focused refinement maps

 

 

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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