Protein docking by the underestimation of free energy funnels in the space of encounter complexes.
Shen Y, Paschalidis ICh, Vakili P, Vajda S, PLoS Comput Biol, 2008 Oct - link

Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels.
Paschalidis ICh, Shen Y, Vakili P, Vajda S, Conf Proc IEEE Eng Med Biol Soc, 2006 - link