Template choice principles
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The most important step of comparative modelling is a carefully done multiple sequence alignment of the target sequence with a protein of known structure. However, you can't expect a useful model either, if you use an unsuitable template and for many templates more than one coordinate file is available.
- All homologues can contribute template information to your project!
- How to find a template
- Keyword searches
- Sequence searches: BLAST and PSI-BAST
- Use of CATH
- Hard and easy results
- % sequence identity and RMSD: choose the most similar model
- Assessing suitability
- Orthology, paralogy
- Complex
- Function (inhibitor?)
- Mutations (incl. His-tag, SeMet, post-translational modifications) - non adapted structural changes
- order
- Crystal packing
- Assessing quality
- Resolution, R-factor and coordinate error
- R-free, R-merge ... but difficult to assess for the non-expert. Best: look at the map, but otherwise may need to check B-factors for sections of interest
