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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. ©CMBI 2002 Relevant topics: Statistics Importance Force fields X-ray NMR How wrong is wrong? ©CMBI 2002 This is wrong, and important. ©CMBI 2002 Planarity force field: many aa are wrong, but often this is not important ©CMBI 2002 MD force field Unlikely becomes wrong if you see it N times ©CMBI 2002 Contact Probability. Force field. Slightly improbable, can only be used protein-wide ©CMBI 2002 DACA ©CMBI 2002 DACA ©CMBI 2002 DACA ©CMBI 2002 DACA ©CMBI 2002 DACA ©CMBI 2002 Contact probability box ©CMBI 2002 His, Asn, Gln ‘flips’. Force field. Most important check for the biologist/user of structures/models ©CMBI 2002 Your best checks include Ramachandran plot (force field): ©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). ©CMBI 2002
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