Flexible molecular superposition: development of a combined similarity index and application of the constrained optimization technique. - Chong Hak Chae; Dong Gweon Oh; Whanchul Shin (J. Comput. Chem., 2001)

Novel Receptor Surface Approach for 3D-QSAR: The Weighted Probe Interaction Energy Method. - Chong Hak Chae; Sung-Eun Yoo; Whanchul Shin (J. Chem. Inf. Model., 2004)

Flexible Alignment of Small Molecules Using the Penalty Method. - Whanchul Shin; Seung Ah Hyun; Chong Hak Chae; Jae Kyung Chon (J. Chem. Inf. Model., 2009)

Binary image representation of a ligand binding site: its application to efficient sampling of a conformational ensemble. - Edon Sung; Sangsoo Kim; Whanchul Shin (BMC Bioinform., 2010)