Assessment scheme

Assessment of the homology model should proceed according to this scheme:

• Compare your initial homology model to the target crystal structure. How well does the model approximate the target? Is it a good model?
• Compare your refined homology model to the target crystal and NMR structures. How well does the refined model approximate the target? Is it a good model?
• Did MD refinement improve the homology model?

 

 

Initial model & target crystal structure

In order to assess how well your initial homology model approximates the target crystal structure, use the three tools discussed on the previous page to gather data about their respective PDB files.

Homology model PDB (final PDB obtained from MOE)

• Use VMD to obtain overlays, relative RMSDs (It can be found in VMD tutorial webpage )
• Use Mol Probity to obtain a Ramachandran plot

Target crystal structure PDB (ID# 2HMB)

• Use VMD to obtain overlays, relative RMSDs
• Use Mol Probity to obtain a Ramachandran plot

 

 

Assignment summary

Report

10 pages, double spaced but not figures and references

Example format:

• Cover page
• Introduction Methods
• Results and Discussion
• Conclusions
• Figures
• References

Presentation

• 20 minutes, with 5 minutes for questions
• Wednesday, April 24
• Include trajectory movie