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Chapter 3: FlexOracle: predicting
flexible hinges by identification of
stable domains
Overview
In the preceding chapter we discussed what various sequence features tell us about the
location of hinges in proteins, and also evaluated the potential for sequence-based hinge
prediction. The use of structural coordinates improves flexibility prediction greatly; we
will now describe the first of several of our methods for predicting hinges with higher
reliability. In Chapter 4 we will show that the method presented here can be combined
with others for improved results.
As discussed earlier, a substantial fraction of protein motions involve hinge bending, and
for these proteins, the accurate identification of flexible hinges connecting rigid domains
would provide significant insight into motion. Programs such as GNM and FIRST have
made global flexibility predictions available at low computational cost, but are not
designed specifically for finding hinge points. In this chapter, accepted for publication in
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