Improvement of protein-compound docking scores by using amino-acid sequence similarities of proteins.
Fukunishi Y, Nakamura H, J Chem Inf Model, 2008 Jan - link

Prediction of protein-ligand complex structure by docking software guided by other complex structures.
Fukunishi Y, Nakamura H, J Mol Graph Model, 2008 Feb - link

Classification of chemical compounds by protein-compound docking for use in designing a focused library.
Fukunishi Y, Mikami Y, Takedomi K, Yamanouchi M, Shima H, Nakamura H, J Med Chem, 2006 Jan 26 - link

A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor.
Tatsumi R, Fukunishi Y, Nakamura H, J Comput Chem, 2004 Dec - link