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©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures. Murphy Introduction X-ray NMR Scores DACA Flips Administration Conclusions

©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

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Page 1: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

Structure validation

Murphy’s law:

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

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 2: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

Why ?

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

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 3: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

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.

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 4: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

What do we check?

Administrative errors.Crystal-specific errors.NMR-specific errors.Really wrong things.Improbable things.Things worth looking at.Ad hoc things.

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 5: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

How difficult can it be?

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 6: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

How difficult can it be?

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 7: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

X-ray specific

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 8: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

X-ray specific

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 9: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

PlanarityMurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 10: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

How wrong is wrong?MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 11: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

Improbable thingsMurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 12: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

Contact Probability

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 13: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

Contact Probability

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 14: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

DACA

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 15: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

DACA

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 16: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

DACA

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 17: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

DACA

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 18: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

DACA

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 19: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

Contact probability box

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 20: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

Using contact probability

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 21: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

His, Asn, Gln ‘flips’MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 22: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

Where are the protons?

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 23: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

Hydrogen bond network

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 24: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

Hydrogen bond force field

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 25: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

Hydrogen bond force field

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 26: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

A typical case: 5TIM

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 27: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

15% should be flipped

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 28: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

Little things hurt bigMurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 29: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

Other errors

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 30: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

Your best checks:MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

DACABackbone normalityand

Page 31: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

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).

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions

Page 32: ©CMBI 2002 Structure validation Murphy’s law: Everything that can go wrong, will go wrong, especially with things as complicated as protein structures

©CMBI 2002

Acknowledgements:

Rob Hooft

MurphyIntroductionX-rayNMRScoresDACAFlipsAdministrationConclusions


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