ONIX: an interactive PC program for the examination of protein 3D structure from PDB.

Abstract

The examination of protein three-dimensional (3D) structure and ligand binding site are the key points in structure-based computer-aided drug design (Kuntz, 1992). The ligand binding site usually consists of some fragments of protein sequence. Its examination requires active participation both of human and computer in the process of investigation. This work is a result of our need for a Windows-based program for such investigations. ONIX is an interactive piece of software based on protein structure hierarchy. Analysis of the molecular surface makes it possible to find all elements of the ligand binding site. ONIX v.1.03 is free software and will be made available by both FTP and E-mail from the EMBL file servers.