l - People

Figure 3.5: Lir-1 (closed) 145
Figure 3.6: cAMP-dependent protein kinase (open) 148
Figure 3.7: Ribose binding protein (open) 151
Figure 3.8: Calmodulin (open, calcium bound form) 154
Figure 4.1: ROC curve for hNMa 212
Figure 4.2: ROC curves for HingeMaster with bootstrapped parameters 213
Figure 4.3: HingeMaster results for individual proteins 215
Figure 4.4: Glutamine Binding Protein (open) 218
Figure 4.5: Human lactoferrin (open, apo form) 221
Figure 4.6: Troponin C (TNC) 225
Figure 4.7: Calmodulin, calcium free (closed) form 227
Figure 4.8: MurA (open form) 229
Figure 5.1: Assignment of residues to S, L, and M. 263
Figure 5.2: Pitch, yaw, and roll definition 263
Figure 5.3: Results for glutamine binding protein 267
Figure 5.4: Results for biotin carboxylase 269
Figure 5.5: Results for Ribose Binding Protein (RBP) 271
Figure 5.6: Results for Adenylate Kinase (ADK) 272
Figure 5.7: Results for MurA 273
Supplementary figure 5.8: Various predictive measures vs. sRMSD, for Glutamine
Binding Protein. 277
Supplementary Figure 5.9: The fitness function vs. sRMSD, for Glutamine Binding
Protein. 278
12