CSB Home | Search | Table of Contents | General Information


APROPOS is a program for the search of pockets in the 3D structure of a molecule. It was developed by Klaus Peters, Jana Fauck and Cornelius Froemmel. A paper describing the program is available in PDF format.

Instructions for use of APROPOS in the CSB core are available.

The program uses the alpha-shape package developed by Herbert Edelsbrunner and Ping Fu.

The alpa-shape of a molecule is calculated from a Delaunay triangluation of the points described by atom coordinates in a PDB file. The alpha-shape obtained with an alpha-value = infinity (convex hull) is compared to the alpha-shape using an alpha-value of approximately 4.5 Å. The population of distance vectors between these two alpha-shapes can be analyzed to obtain potential pockets on the surface of the molecule. The following diagram from the paper by Peters et al. illustrates the method.

CSB Home | Search | Table of Contents | General Information
Center for Structural Biology (www.csb.yale.edu), Yale University (www.yale.edu)
Contact: webadmin(at)mail^csb^yale^edu
Last Modified: Wednesday, 21-Aug-2002 13:38:29 EDT by P. Fleming