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

List of Figures
1.1 The standard amino acids . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
1.2 Examples of functional sites in proteins . . . . . . . . . . . . . . . . . . . . 18
1.3 The protein universe and its knowledge representation . . . . . . . . . . . . 20
2.1 Data banks in the protein universe . . . . . . . . . . . . . . . . . . . . . . 28
2.2 Three hyperlinked protein data banks . . . . . . . . . . . . . . . . . . . . . 29
2.3 Categories for protein sequence annotation UniProtKB . . . . . . . . . . . 32
2.4 GO terms are not suitable for protein residue annotation . . . . . . . . . . 34
3.1 Overview of processes and evaluation methods of the developed 3D pattern
identification system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
3.2 Four classes of interactions within a 3-body . . . . . . . . . . . . . . . . . . 49
3.3 Non-redundant structure set for 3D pattern mining . . . . . . . . . . . . . 53
3.4 Distribution analysis of extracted residue triplets . . . . . . . . . . . . . . 57
3.5 Comparison of extracted residue triplets based on their interaction type . . 58
3.6 The effect of varying the cross-validation sample size on significance testing
of residue interaction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
4.1 A metal binding site with the 3Cys pattern in OLDFIELD . . . . . . . . . 68
4.2 A metal binding site with the Cys-2His pattern in OLDFIELD . . . . . . . 69
4.3 A metal binding site with the 3Cys pattern in SCOP40 . . . . . . . . . . . 70
4.4 A metal binding site with the Cys-2His pattern in SCOP40 . . . . . . . . . 71
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