26. Structural Validation of Homology
19% Seq ID
Z = 12.2
Adenylate Kinase Guanylate Kinase

28. Dali Domain Dictionary Deitman, Park, Notredame, Heger, Lappe, and Holm Nucleic Acids Res. 29: 5557 (2001)
Dali Domain Dictionary is a numerical taxonomy of all known domain structures in the PDB
Evolves from Dali / FSSP Database
Holm & Sander, Nucl. Acid Res. 25: (1997)
Dali Domain Dictionary Sept 2000
10,532 PDB enteries
17,101 protein chains
5 supersecondary structure motifs (attractors)
1375 fold types
2582 functional families
3724 domain sequence families

29. courtesy of C. Chothia

30. Most proteins in biology have been produced by the duplication,
divergence and recombination of
the members of a small number of
protein families.
courtesy of C. Chothia

31. courtesy of C. Chothia

32. courtesy of C. Chothia

33. courtesy of C. Chothia

34. courtesy of C. Chothia

35. Cadherins
courtesy of C. Chothia

36. courtesy of C. Chothia

37. courtesy of C. Chothia

38. A Global Representation of Protein Fold Space Hou, Sims, Zhang, Kim, PNAS 100: 2386 - 2390 (2003)
Database of 498 SCOP “Folds” or “Superfamilies”
The overall pair-wise comparisons of 498 folds lead to a 498 x 498 matrix of similarity scores Sijs, where Sij is the alignment score between the ith and jth folds.
An appropriate method for handling such data matrices as a whole is metric matrix distance geometry . We first convert the similarity score matrix [Sij] to a distance matrix [Dij] by using Dij = Smax - Sij, where Smax is the maximum similarity score among all pairs of folds.
We then transform the distance matrix to a metric (or Gram) matrix [Mij] by using Mij = Dij2 - Dio2 - Djo2
where Di0, the distance between the ith fold and the geometric centroid of all N = 498 folds. The eigen values of the metric matrix define an orthogonal system of axes, called factors. These axes pass through the geometric centroid of the points representing all observed folds and correspond to a decreasing order of the amount of information each factor represents.

39. A Global Representation of Protein Fold Space Hou, Sims, Zhang, Kim, PNAS 100: 2386 - 2390 (2003)