1. Homology modelling ? X-ray ? NMR ?

2. Homology Modelling !

3. Data ~ infinite…

4. Helices are Helices

5. Strands are Strands

6. What can be Modelled ?

8. Modelling beats X-ray

9. The ‘8’ Steps of Modelling 1 Detect template 2 Get alignment 3 Optimize alignment 4 Optimize template 5 Exchange side chains 6 Deal with insertions/deletions 7 Optimize model 8 Validate 9 Iterate

10. Template detection Normally BLAST is good enough. If BLAST doesn’t find a template, You should not want to build a model. When desperate, use PSI-BLAST (on PDB + SwissProt), or use threading.

11. Threading Two aligned ‘proteins’

12. The ‘8’ Steps of Modelling 1 Detect template 2 Get alignment 3 Optimize alignment 4 Optimize template 5 Exchange side chains 6 Deal with insertions/deletions 7 Optimize model 8 Validate 9 Iterate

13. How to align: ASASASASASAS YPYPYPYPYPYP (three ways…)

14. How to align: ASASASASASAS- AYAYAYAYAYAY- -YPYPYPYPYPYP (two ways…)

15. The ‘8’ Steps of Modelling 1 Detect template 2 Get alignment 3 Optimize alignment 4 Optimize template 5 Exchange side chains 6 Deal with insertions/deletions 7 Optimize model 8 Validate 9 Iterate

16. Alignment optimization 1 Use threading techniques. 2 Shift gaps around:

17. The ‘8’ Steps of Modelling 1 Detect template 2 Get alignment 3 Optimize alignment 4 Optimize template 5 Exchange side chains 6 Deal with insertions/deletions 7 Optimize model 8 Validate 9 Iterate

18. Select ‘best’ template http://swift.cmbi.ru.nl/gv/pdbreport/

19. Deal with errors

20. The ‘8’ Steps of Modelling 1 Detect template 2 Get alignment 3 Optimize alignment 4 Optimize template 5 Exchange side chains 6 Deal with insertions/deletions 7 Optimize model 8 Validate 9 Iterate

21. Position specific rotamers

24. The ‘8’ Steps of Modelling 1 Detect template 2 Get alignment 3 Optimize alignment 4 Optimize template 5 Exchange side chains 6 Deal with insertions/deletions 7 Optimize model 8 Validate 9 Iterate

25. Insertions - Deletions Insertions are impossible Deletions: Move gap around in template till end point distance is short. If this is not possible, you have either the wrong template, or the wrong alignment.

26. The ‘8’ Steps of Modelling 1 Detect template 2 Get alignment 3 Optimize alignment 4 Optimize template 5 Exchange side chains 6 Deal with insertions/deletions 7 Optimize model 8 Validate 9 Iterate

27. Model Optimization Do NOT use standard molecular dynamics: And when you use waters, the crystallographer is ready before you are

28. Model Optimization Use 25 – 50 steps energy minimization, or use a force field that has been especially designed for the optimization of homology models.

29. The ‘8’ Steps of Modelling 1 Detect template 2 Get alignment 3 Optimize alignment 4 Optimize template 5 Exchange side chains 6 Deal with insertions/deletions 7 Optimize model 8 Validate 9 Iterate

30. Results ???

33. WWW This seminar is available (free from restrictions) at: http://swift.cmbi.ru.nl/gv/seminars/