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SuperPose: A Web Server for Automated Protein Structure Superposition

SuperPose: A Web Server for Automated Protein Structure Superposition

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## SuperPose: A Web Server for Automated Protein Structure Superposition

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**1. **SuperPose: A Web Server for Automated Protein Structure Superposition Gary Van Domselaar
gvd@redpoll.pharmacy.ualberta.ca
October 08, 2004

**2. **Introduction Who Cares?
Review of Superposition
Identifying Corresponding Points Between Structures
Multiple Structure Superposition
RMSD Calculation
The SuperPose Web Site

**3. **Who Cares? NMR Spectroscopists

**4. **Who Cares? Structural Biologists

**5. **Who Cares? Evolutionary Biologists

**6. **Principles of Superposition How do we superimpose these two cubes?

**7. **Principles of Superposition Identify corresponding points.

**8. **Principles of Superposition Identify the common center and the principle axes for each structure.

**9. **Principles of Superposition Translate the two structures so their centers overlap.

**10. **Principles of Superposition Rotate the two structures so the average distance between corresponding points is minimized,and their principal axes overlap.

**11. **Principles of Superposition Rotations can be accomplished by multiplying each atom coordinate with an appropriate rotation matrix, but this is slow:

**12. **Principles of Superposition A faster way is to use quaternion-based superposition to both rotate and minimize the sum of residuals
S.K.Kearsley, On the orthogonal transformation used for structural comparisons, Acta Cryst. A45, 208 (1989)
http://www-structure.llnl.gov/xray/comp/suptext.htm

**13. **Identifying Corresponding Points Between Protein Structures Sequence Alignment

**14. **Identifying Corresponding Points Between Protein Structures Problem: Low Homology

**15. **Identifying Corresponding Points Between Protein Structures Solution: Secondary Structural Alignment

**16. **Identifying Corresponding Points Between Protein Structures Problem: Multiple Structural Forms

**17. **Identifying Corresponding Points Between Protein Structures Solution: Subdomain Alignment

**18. **Identifying Corresponding Points Between Protein Structures The Difference Distance Matrix
Make a Distance Matrix for each structure:

**19. **Identifying Corresponding Points Between Protein Structures The Difference Distance Matrix
Subtract the dif matrices to make a DD Matrix
Plot the magnitude of the distance as a color shade

**20. **Identifying Corresponding Points Between Protein Structures Analyze the difference distance matrix for similar subdomains.
The DD Matrix will have regions that are similar, and regions that are different.

**21. **Identifying Corresponding Points Between Protein Structures

**22. **Identifying Corresponding Points Between Protein Structures

**23. **Identifying Corresponding Points Between Protein Structures

**24. **Multiple Structure Superposition How do you optimally superimpose more than 2 structures?

**25. **Multiple Structure Superposition Superimpose to an average structure

**26. **Multiple Structure Superposition Superposition ordering is important
Structures should be superposed in order of their pairwise structural similarity.
An 'all-against-all' DD Matrix analysis can be used to quickly determine overall relative similarity between every pair of structures

**27. **Multiple Structure Superposition A structure 'pileup' is created from the DD Matrix analysis to determine the superposition order.

**28. **Multiple Structure Superposition Average structures can be sensibly generated only from a collection of structures with identical sequences
How do you superimpose a collection of sequences with non-identical sequences?
Progressive pairwise buildup using the pileup as a guide.

**29. **Multiple Structure Superposition

**30. **RMSD Calculation The degree of similarity between two or more structures is described by its average root mean square deviation (RMSD):

**31. **SuperPose http://wishart.biology.ualberta.ca/SuperPose/
Superposition for 2 chains and for multiple chains
Subdomain superposition
Superposition of structures with low sequence identity