Development and validation of a modular, extensible docking program: DOCK 5.
Moustakas DT, Lang PT, Pegg S, Pettersen E, Kuntz ID, Brooijmans N, Rizzo RC, J Comput Aided Mol Des, 2006 Oct-Nov - link

Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit.
Pan H, Agarwalla S, Moustakas DT, Finer-Moore J, Stroud RM, Proc Natl Acad Sci U S A, 2003 Oct 28 - link