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Conclusions 279
References 281
Table of figures
Figure 1.1: The new morph page. 38
Figure 1.2: The motion of an ethane molecule as determined by geometric simulation in
FRODA. 39
Figure 1.3: Conformational change and functional grouping. 40
Figure 2.1: Residue type 85
Figure 2.2: Distance from active sites 86
Figure 2.3: Secondary structure 87
Figure 2.4: Physicochemical properties 88
Figure 2.5: Conservation: full set 89
Figure 2.6: Conservation: enzymes dataset 90
Figure 2.7: Solvent accessible surface area 91
Figure 2.8: ROC curve for HingeSeq 92
Figure 2.9: Amino acid composition of MolMovDB vs. PDB 93
Figure 2.10: Overlap between manual and computer annotated datasets 94
Figure 2.11: Resampling of glycine occurrence in hinge vs. non-hinge residues 95
Figure 3.1: Fragmenting the protein 136
Figure 3.2: Results for individual proteins 137
Figure 3.3: Folylpolyglutamate Synthetase (closed) 139
Figure 3.4: AMPA Receptor GluR2 (closed) 142
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