Abstract
Our database contains three-dimensional pharmaceutical structures simulated and optimized with the molecular modeling software Macromodel. The database has been compiled from the compounds contained in "Drug in Japan: Ethical Drugs", edited by the Japan pharmaceutical information center (Tokyo, Japan) in the initial stage of its development. The three-dimensional models were stored on the Web server where they can be viewed, rotated, and animated by the client with either the plug-in, Chemscape Chime, or the Java Applet, Chemis3D. We applied a molecular dynamics simulation to the molecular motion trajectories; three-dimensional animation demonstrates the actual movement and rotation of molecules on their bond axes. This database provides both zipped coordination files indicating conformational distribution for each drug and zipped virtual reality modeling language (VRML) files indicating its electrostatic potential mapped on the electron density surface. A search of the pharmaceutical structures can be conducted through drawing of partial plane structures or input of general names with JChem software to the SQL server containing fully optimized structural data.
