TOPS protein topology search, pattern discovery, and structure comparison http://tops.ebi.ac.uk/tops

06/12/99


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Table of Contents

  1. TOPS protein topology search, pattern discovery, and structure comparison http://tops.ebi.ac.uk/tops

  2. Collaborators

  3. Acknowledgements

  4. Outline

  5. TOPS

  6. Motivtion

  7. Protein patterns (motifs)

  8. Topological description

  9. Secondary Structures Elements

  10. A plait

  11. PPT Slide

  12. Generating TOPS diagrams

  13. Formal definitions

  14. Prolog domain description Databases: Atlas 3000 (2MB), PDB 15000+ (11MB)

  15. Plait motif

  16. Plait formal definition

  17. Pattern matching

  18. Matching algorithm

  19. Topological search with plait motif

  20. Searching the TOPS atlas

  21. Topological pattern discovery (pattern extension and repeated matching)

  22. PPT Slide

  23. Discovering common patterns and making multiple alignments

  24. Topological pattern discovery - maximal cliques

  25. Complexity of pattern discovery

  26. CATH hierarchy

  27. CATH database hierarchy

  28. Characterisation of CATH/SCOP

  29. Pattern discovery

  30. Outliers!

  31. Restricting the learning set

  32. Learning CATH patterns

  33. Structure comparison

  34. Using a pattern to compare 2 structures

  35. Topological structure comparison: 2bop

  36. Dendrogram of comparisons

  37. Visualisation of pairwise comparisons (CATH representatives)

  38. Evaluating the results (DRG)

  39. Summary

  40. Future work

  41. Resources

 Author: drg

Email: drg@cs.city.ac.uk

Home Page: http://www.cs.city.ac.uk/~drg