Clashes
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(New page: ''Clashes'' in protein models, also called ''steric clashes'', occur when two non-bonded atoms are impossibly close to each other. This happens when the van der Waals radii of the atoms ov...)
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Revision as of 18:53, 6 November 2021
Clashes in protein models, also called steric clashes, occur when two non-bonded atoms are impossibly close to each other. This happens when the van der Waals radii of the atoms overlap; that is, when two atoms are occupying the same space. Clashes typically occur in lower resolution models due to the difficulties of obeying all chemical constraints while optimizing the fit of the model to the experimental data. Clashes are more common in X-ray crystallographic models with resolutions of 3.0 Å or worse, or in cryo-EM models. (NMR models generally lack clashes because they are forced to obey chemical constraints.)
The presence of too many clashes in a model calls into question its reliability. All models submitted to the Protein Data Bank (PDB) are analyzed by MolProbity, which determines a clash score, and ranks it relative to other models of the same resolution. Each PDB entry has an extensive quality report. Here are a couple of examples:
Visualization of Clashes
- MolProbity offers visualization of clashes in
- Jmol offers visualization of clashes
