TY - JOUR T1 - Computing and displaying intermolecular negative volume for docking JF - Scientific visualization: the visual extraction of knowledge from data Y1 - 2006 A1 - Lee,C. A1 - Varshney, Amitabh AB - Protein docking is a Grand Challenge problem that is crucial to our understanding of biochemical processes. Several protein docking algorithms use shape complementarity as the primary criterion for evaluating the docking candidates. The intermolecular volume and area between docked molecules is useful as a measure of the shape complementarity. In this paper we discuss an algorithm for interactively computing intermolecular negative volume and the area of docking site using graphics hardware. We also present the design considerations for building an interactive 3D visualization tool for visualizing intermolecular negative volumes. VL - I M3 - 10.1007/3-540-30790-7_4 ER -