Automatic functional annotation of predicted active sites - European ...

List of Tables
3.1 Study on the effect of varying the interaction distance threshold in structure
triangulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
4.1 Summary of extracted data at each protein structure data mining step . . 65
4.2 Identification of metal binding sites in OLDFIELD . . . . . . . . . . . . . 66
4.3 Convergent metal binding sites identified in SCOP40 . . . . . . . . . . . . 72
4.4 List of cross-validated active site residues . . . . . . . . . . . . . . . . . . . 74
4.5 Extending the catalytic triad into 4-bodies . . . . . . . . . . . . . . . . . . 76
5.1 Regular expression patterns for the detection of residue mentions in text . 84
5.2 Performance evaluation of residue entity recognition . . . . . . . . . . . . . 90
5.3 Performance evaluation of protein entity recognition . . . . . . . . . . . . . 91
5.4 Performance evaluation of organism entity recognition . . . . . . . . . . . . 91
5.5 Performance evaluation of residue-protein-organism entity association detection
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
5.6 Performance evaluation of protein-organism and protein-residue entity association
detections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
5.7 A specialised performance evaluation between GC and XC2. . . . . . . . . 94
6.1 Biological categories for the classification of protein residue related information
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
6.2 Category distribution in the text feature reference set . . . . . . . . . . . . 115
13