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hinges. Kundu et al. use the lowest order nontrivial mode to assign residues to one of
two structural domains according to the sign of the displacement, and also perform some
physically motivated postprocessing of the results.
Similarly, much work has been done to solve the related problem of finding domain
boundaries, which can be flexible or inflexible. Nagarajan and Yona[33] have shown
how to analyze multiple sequence alignments to identify domains. Marsden et al showed
that predicted secondary structure could help find domain boundaries. Jones et al.
combined PUU[35], DETECTIVE[36], and DOMAK[37] to make a powerful domain
boundary predictor[38]. Domain boundaries, again, are not necessarily flexible, and
furthermore many of these methods require a multiple sequence alignment which cannot
always be obtained. Given the difficulty of observing motion by experimental means and
the limited accuracy or applicability of existing computational methods, there is a need
for improved techniques for predicting motion.
45% of motions in a representative set from the Database of Macromolecular Motions
have been found to move by a hinge bending mechanism [3, 9, 25]. Keating et al.(in
preparation) found that interpretation of hydrogen-bond dilution plots produced by
FIRST[32] could discriminate domain hinge bending from fragment motions with some
accuracy, even when the motion itself was unknown. For hinge bending proteins, if the
location of the hinge could be predicted given a single set of structural coordinates,
significant insight could be gained into possible movements.
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