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lowered, and the area under the curve will be significantly greater than 0.5. The ROC
curve is shown in Figure 2.8. Although work remains to be done before sequence-based
hinge prediction can be relied upon exclusively, HingeSeq displays significant ability to
detect potential for flexibility.
Checking for dataset bias
These findings assume that the dataset used does not contain significant bias or artifacts,
either in the composition of the entire dataset or of the hinges within it. To substantiate
this, we performed various studies as follows.
Bias in amino acid composition and functional classification
In order to find out whether the MolMovDB database contained any bias in amino acid
composition, we extracted the sequences of all the morphs in MolMovDB and counted
the total occurrence of each residue type. Suspecting that redundancies might bias the
result, we clustered the sequences and recounted the amino acid residues in the same
way. We compared these numbers to publicly available amino acid frequencies of
occurrence for the PDB (Protein Data Bank)[5] (Figure 2.9). The amino acid frequency
of occurrence for the clustered MolMovDB morphs was found to be essentially that of
the PDB, from which it was created, therefore no particular database bias is in evidence.
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