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List of Figures

1. The dynamic programming algorithm
2. Definitions of molecular surfaces
3. Analysis of light chain antigen contacts
4. Analysis of heavy chain antigen contacts
5. CDR arrangement
6. Antigen contacts and CDR conformation
7. Antigen contacts compared between different loop conformations
8. Combining site shape analysis
9. Antigen binding pocket prediction
10. Reducing noise in the prediction datasets
11. Reliability measures for class predictions
12. Common mainly-$\beta$ architectures
13. Location of significant sequence patterns in protein structures
14. Fold recognition performance using hydrophobicity and conservation
15. Fold recognition performance using hydrophobicity and DSC secondary structure predictions
16. Summary statistics of fold recognition trials
17. Plots of fold recognition results vs. structural similarity measures
18. Kohonen map overview
19. Mapping of domain 1cgt04 three-dimensional coordinates
20. Mapping of domain 1ghsA0 three-dimensional coordinates
21. Distance matrix from self-organising map
22. Mapping discontinuities
23. Protein shape and map dimensions
24. Sequence derived hydropathy for 1sxaA0
25. Structure/Hydropathy mapping (i)
26. Structure/Hydropathy mapping (ii)
27. Hydropathy mapping of a selection of domains
28. Mapping sequence conservation and structure
29. Fold recognition performance using structure-mapped hydrophobicity information
30. Alignment quality for 50 mapping replicates vs. unmapped results
31. Alignment shifts with different gap penalties.
32. Multiple sequence gathering overview
33. Weeding multiple sequences