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Structure validationStructure validation
Everything that can go wrong, will Everything that can go wrong, will go wrong, especially with things as go wrong, especially with things as complicated as protein structures.complicated as protein structures.
Why ?Why ?
Why does a sane (?) human being spend fourteen years to search for millions of errors in the PDB?
Because:Because:
Everything we know about proteins comes from PDB files.
If a template is wrong the model will be wrong.
Errors become less dangerous when you know about them.
What do we check?What do we check?
Administrative errors.Crystal-specific errors.NMR-specific errors.Really wrong things.Improbable things.Things worth looking at.Ad hoc things.
How difficult can it be?How difficult can it be?
How difficult can it be?How difficult can it be?
Contact ProbabilityContact Probability
Contact ProbabilityContact Probability
DACADACA
DACADACA
DACADACA
DACADACA
DACADACA
Contact probability boxContact probability box
Using contact probabilityUsing contact probability
Other errorsOther errors
His, Asn, Gln ‘flips’His, Asn, Gln ‘flips’
Where are the protons?Where are the protons?
Hydrogen bond networkHydrogen bond network
Hydrogen bond force fieldHydrogen bond force field
Hydrogen bond force fieldHydrogen bond force field
A typical case: 5TIMA typical case: 5TIM
A typical case: 5TIMA typical case: 5TIM
15% should be flipped15% should be flipped
Little things hurt bigLittle things hurt big
Improbable thingsImprobable things
Your best check:Your best check:
PlanarityPlanarity
How wrong is wrong?How wrong is wrong?
ConclusionsConclusions
Everything that could go wrong has gone wrong.Errors are on a ‘sliding scale’.Error detection can detect a lot, but surely not everything (yet).
Acknowledgements:Acknowledgements:
Rob Hooft
