A new molecular simulation software package - Peking University Drug Design System (PKUDDS) for structure-based drug design

摘要

We present a comprehensive molecular simulation program package, the Peking University Drug Design System (PKUDDS), which runs on personal computers. PKUDDS has been developed mainly for computer-aided drug design using the methods of two-dimensional quantitative structure-activity relationship, three-dimensional quantitative structure-activity relationships, molecular docking, and database screening. This study presents an overview of its functionality, especially of methods developed in our group. PKUDDS uses genetic algorithms in molecular docking, conformational analysis,a nd quantitative structure-lactivity relationships as the most useful optimization technique. A user-friendly graphical interface provides easy access to many function of PKUDDS. We report some examples of our considerable research using PKUDDS.