Figure 1.

Fuzzle database construction and content. (a) Database construction. Domain sequences and structures from SCOP95 were used as input. Sequence profile HMMs were generated for each domain and compared all-against-all. Matches between pairs of domains were structurally superimposed. The sequence and structural data collected for each pair constitutes a hit, which is stored in Fuzzle, summing up to more than 8 million pairwise hits. (b) Contents of a hit. Each hit in Fuzzle contains information about the two domains (query and subject), start and end of the fragment they share, HHsearch probability, and RMSD, among others. (c) Distribution of hits according to their probability and TM-score. The majority of hits present probabilities below 35% but there is also a non-negligible portion of hits with high probability and TM-score. Hits in this upper right quadrant (probabilities > 70% and TM-scores > 0.3) were plotted with their probabilities versus lengths (d).