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Using internal and collective variables in Monte Carlo simulations of nucleic acid structures: Chain breakage/closure algorithm and associated Jacobians.
Sklenar, H., Wuestner, D. and Rohs, R.
Journal of Computational Chemistry 27 (3): 309-315. February 2006

Harmonic modes as variables to approximately account for receptor flexibility in ligand-receptor docking simulations: application to DNA minor groove ligand complex.
Zacharias, M. and Sklenar, H.
Journal of Computational Chemistry 20 : 287-300. 1 February 1999