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

Docking of protein molecular surfaces with evolutionary trace analysis.
Kanamori E, Murakami Y, Tsuchiya Y, Standley DM, Nakamura H, Kinoshita K, Proteins, 2007 Dec 1 - 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

Protein-inhibitor flexible docking by a multicanonical sampling: native complex structure with the lowest free energy and a free-energy barrier distinguishing the native complex from the others.
Kamiya N, Yonezawa Y, Nakamura H, Higo J, Proteins, 2008 Jan 1 - link

Flexible docking of an amyloid-forming peptide from beta(2)-microglobulin.
Standley DM, Yonezawa Y, Goto Y, Nakamura H, FEBS Lett, 2006 Nov 13 - 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