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PDB ID vs. morph ID BLAST features 35
Tools relating Motion to Sites on Structure 36
Catalytic site highlighting 36
Conservation score viewer 37
Figures 38
Chapter 2: Hinge Atlas: relating protein sequence to sites of structural flexibility 43
Overview 43
Background 46
Methods 52
Preparation of computer annotated hinge dataset 52
The Hinge Annotation Tool 51
Construction of the Hinge Atlas 55
Availability of datasets 58
Method for analyzing relative frequency of occurrence 60
Results 64
Are certain amino acids more likely to occur in hinges? 64
Are residues within a certain distance of an active site more likely to be hinge residues?
64
Are hinges segregated by secondary structure? 66
Are certain physicochemical properties preferred in hinge residues? 67
Are hinge residues conserved in evolution? 68
Are hinge residues more likely to occur on the surface? 72
How many hinge sites appear in each protein? 72
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