SDOVS: a solvent dipole ordering-based method for virtual screening.
We previously reported that solvent dipole ordering (SDO) at the ligand binding site of a protein indicates an outline of the preferred shape and binding pose of the ligands. We suggested that SDO-mimetic pseudo-molecules that mimic the 3D shape of the SDO region could be used as molecular queries with a shape similarity matching method in virtual screening. In this work, a virtual screening method based on SDO, named SDOVS, was proposed. This method was applied to virtual screening of ligands for four typical drug target proteins and the performance compared with that of FRED (well-known rigid docking method); the efficiency of SDOVS was demonstrated to be better than FRED.
Murata
Katsumi
K
Department of Theoretical Drug Design, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan. murata@pharm.kyoto-u.ac.jp
Nagata
Naoya
N
Nakanishi
Isao
I
Kitaura
Kazuo
K
D000465:Algorithms; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D015195:Drug Design; D055808:Drug Discovery; D008024:Ligands; D056004:Molecular Dynamics Simulation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D054852:Small Molecule Libraries / Q000494:pharmacology; D012997:Solvents / Q000737:chemistry*
D008024:Ligands; D011506:Proteins; D054852:Small Molecule Libraries; D012997:Solvents