Structure validation Everything that can go wrong, will go wrong, especially with things as complicated as protein structures. Everything that can go wrong,

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Presentation transcript:

Structure validation Everything that can go wrong, will go wrong, especially with things as complicated as protein structures. Everything that can go wrong, will go wrong, especially with things as complicated as protein structures.

Why ? Why does a sane (?) human being spend fourteen years to search for millions of errors in the PDB?

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? 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?

Contact Probability

DACA

DACA

DACA

DACA

DACA

Contact probability box

Using contact probability

Other errors

His, Asn, Gln ‘flips’

Where are the protons?

Hydrogen bond network

Hydrogen bond force field

A typical case: 5TIM

15% should be flipped

Little things hurt big

Improbable things

Your best check:

Planarity

How wrong is wrong?

Conclusions 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: Rob Hooft