Computational prediction of ion permeation characteristics in the glycine receptor modified by photo-sensitive compounds. - Mary Hongying Cheng; Robert D. Coalson; Michael Cascio; Maria G. Kurnikova (J. Comput. Aided Mol. Des., 2008)

Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle. - Mary Hongying Cheng; Ivet Bahar (PLoS Comput. Biol., 2014)

Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model. - Avisek Das; Mert Gur; Mary Hongying Cheng; Sunhwan Jo; Ivet Bahar; Benoît Roux (PLoS Comput. Biol., 2014)