Conformational analysis of three pyrophosphate model species: Diphosphate, methyl diphosphate, and triphosphate. - Ming-Jing Hwang; Pei-Ying Chu; Jye-Chan Chen; Ito Chao (J. Comput. Chem., 1999)

SLITHER: a web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating through channels in membrane transporters. - Po-Hsien Lee; Kuei-Ling Kuo; Pei-Ying Chu; Eric Minwei Liu; Jung-Hsin Lin (Nucleic Acids Res., 2009)

idTarget: a web server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach. - Jui-Chih Wang; Pei-Ying Chu; Chung-Ming Chen; Jung-Hsin Lin (Nucleic Acids Res., 2012)