ELECT++: Faster conformational search method for docking flexible molecules using molecular similarity. - Shingo Makino; Irwin D. Kuntz (J. Comput. Chem., 1998)

DREAM++: Flexible docking program for virtual combinatorial libraries. - Shingo Makino; Todd J. A. Ewing; Irwin D. Kuntz (J. Comput. Aided Mol. Des., 1999)

DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases. - Todd J. A. Ewing; Shingo Makino; A. Geoffrey Skillman; Irwin D. Kuntz (J. Comput. Aided Mol. Des., 2001)

Discovery of a novel serine protease inhibitor utilizing a structure-based and experimental selection of fragments technique. - Shingo Makino; Takashi Kayahara; Kazumi Tashiro; Mitsuo Takahashi; Takashi Tsuji; Masataka Shoji (J. Comput. Aided Mol. Des., 2001)