The citation for StoneHinge is:
Keating KS, Flores SC, Gerstein MB, Kuhn LA (2009). StoneHinge: Hinge Prediction by Network Analysis of Individual Protein Structures. Protein Science 18: 359-371.
StoneHinge also makes use of a number of additional software packages. Citations for these are:
ProFlex
Jacobs DJ, Rader AJ, Kuhn LA, and Thorpe MF (2001). Protein flexibility predictions using graph theory. Proteins 44: 150-165.
DomDecomp
Kundu S, Sorensen DC, and Phillips GN, Jr (2004). Automatic domain decomposition of proteins by a Gaussian Network Model. Proteins 57: 725-733.
GROMACS
Berendsen HJ, van der Spoel D, and van Drunen R (1995). GROMACS: A message-passing parallel molecular dynamics implementation. Computer Physics Communications 91: 43-56.