3DFS: a new 3D flexible searching system for use in drug design

This paper describes a new 3D flexible searching system 3DFS which supports two types of query definitions: simple atom-based definition and generalized function-based definition. The simple and practical definitions of hydrogen bond acceptors/donors, charge centers, aromatic ring centers, and a rapid hydrophobe recognition algorithm are described in detail. 3DFS adopts a four-step searching strategy: a rapid ID screening, an exact 2D substructure searching using the GMA algorithm, a rigid 3D searching, and a conformationally flexible 3D searching using POWELL method. The utility of 3DFS is illustrated by several typical searching examples.