1. NMR ? X-ray ? Homology modelling ? Intro Proteins Modelling 8 Steps
Detect
Threading
Alignment
Template
Side chain
Indels
Optimize
Validate
Iterate
NMR ?
X-ray ?
©CMBI 2002

2. Homology Modelling !
©CMBI 2002

3. Homology Modelling
Video seminar (7minutes) in the course ‘Protein Structure seminars’.
©CMBI 2002

4. Homology Modelling
Main concept is to take a template, and to make minimal modifications to arrive at the model.
Think about:
Insertions and deletions best done by brain power;
Errors in template likely become errors in model;
At >75% sequence identity between template and model, nearly all homology modelling packages are equally good (bad);
Energy minimisations tend to not make the model better;
The template structure sits in a crystal, the model not;
Even the template structure is a model.
©CMBI 2002