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SuperPose: A Web Server for Automated Protein Structure Superposition

Lab Meeting 10/08/2004. 13. Identifying Corresponding Points Between Protein Structures ... Lab Meeting 10/08/2004. 20. Identifying Corresponding Points Between Protein Structures ...

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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

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