1. Applications of Homology Modeling
Hanka Venselaar

2. This seminar…. Homology Modeling… Why? What? When? How?
And a few real world examples….

3. * Homology modeling O % identity # residues
* Actually, modelling is possible, but we cannot get an alignment…
Example: by 80 residues  30% identity sufficient

4. Homology modeling in short…
Prediction of structure based upon a highly similar structure ?
Unknown structure
NSDSECPLSHDG
NSDSECPLSHDG
|| || | ||
NSYPGCPSSYDG
Alignment of model and template sequence
Back bone copied
Known structure
Model!
Copy backbone and conserved residues
Add sidechains, Molecular Dynamics simulation on model
Known structure

5. The 8 steps of Homology modeling

6. 1: Template recognition and initial alignment

7. 1: Template recognition and initial alignment
BLAST your sequence against PDB
Best hit  normally template
Initial alignment 
NSDSECPLSHDGYCLHDGVC
|| || | ||||| |||
NSYPGCPSSYDGYCLNGGVC

8. 1: Template recognition and initial alignment
2: Alignment correction
1: Template recognition and initial alignment

9. 2: Alignment correction
Functional residues  conserved
Use multiple sequence alignments
Deletions  shift gaps
CPISRTAAS-FRCW
CPISRTG-SMFRCW
CPISRTA--TFRCW
CPISRTAASHFRCW
CPISRTGASIFRCW
CPISRTA---FRCW
Multipe sequence alignment
Correct alignment
 Sequence with known structure
Your sequence
CPISRTGASIFRCW CPISRTGASIFRCW
CPISRTA---FRCW CPISRT---AFRCW
Both are possible

10. 2: Alignment correctionS G P L A E R C I V C R M P E V C R M P E
-A-V
F-D-
Core residues  conserved
Use multiple sequence alignments
Deletions in your sequence  shift gaps
Known structure FDICRLPGSAEAV
Model FNVCRMP---EAI
Model FNVCR---MPEAI
 Correct alignment

11. 1: Template recognition and initial alignment
2: Alignment correction
1: Template recognition and initial alignment
3: Backbone generation

12. 3: Backbone generation Making the model….
Copy backbone of template to model
Make deletions as discussed
(Keep conserved residues)

13. 1: Template recognition and initial alignment
2: Alignment correction
1: Template recognition and initial alignment
4: Loop modeling
3: Backbone generation

14. 4: Loop modeling Known structure GVCMYIEA---LDKYACNC
Your sequence GECFMVKDLSNPSRYLCKC
Loop library,
try different options

15. 1: Template recognition and initial alignment
2: Alignment correction
1: Template recognition and initial alignment
3: Backbone generation
4: Loop modeling
5: Sidechain modeling

16. 5: Side-chain modeling Several options
Libraries of preferred rotamers based upon backbone conformation

17. 1: Template recognition and initial alignment
2: Alignment correction
1: Template recognition and initial alignment
3: Backbone generation
4: Loop modeling
5: Sidechain modeling
6: Model optimization

18. 6: Model optimization Molecular dynamics simulation Remove big errors
Structure moves to lowest energy conformation

19. 1: Template recognition and initial alignment
2: Alignment correction
1: Template recognition and initial alignment
3: Backbone generation
4: Loop modeling
5: Sidechain modeling
7: Model validation
6: Model optimization

20. 7: Model Validation Second opinion by PDBreport /WHATIF
Errors in active site?  new alignment/ template
No errors?  Model!

21. 1: Template recognition and initial alignment
2: Alignment correction
1: Template recognition and initial alignment
3: Backbone generation
4: Loop modeling
8: Iteration
8: Iteration
5: Sidechain modeling
8: Iteration
8: Iteration
7: Model validation
6: Model optimization

22. 1: Template recognition and initial alignment
2: Alignment correction
1: Template recognition and initial alignment
3: Backbone generation
4: Loop modeling
8: Iteration
8: Iteration
5: Sidechain modeling
Model!
8: Iteration
8: Iteration
7: Model validation
6: Model optimization

23. 8 steps of homology modeling
1: Template recognition and initial
alignment
2: Alignment correction
3: Backbone generation
4: Loop modeling
5: Side-chain modeling
6: Model optimization
7: Model validation
8: Iteration
Alignment
Modeling
Correction

24. To conclude…. Homology Modeling…
What? Prediction of an unknown structure based on an homologous and known structure
Why? To answer biological and medical questions when the “real” structure is unknown
When? A template with enough identity must be available
How? 8 Steps

25. And now….
After the next seminar go to the course website:
Thanks to Hanka Venselaar for making nearly all slides in this seminar.