Computing and Displaying Intermolecular Negative Volume for Docking

  • Chang Ha Lee
  • Amitabh Varshney
Conference paper
Part of the Mathematics and Visualization book series (MATHVISUAL)


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.


Molecular Surface Docking Site Graphic Hardware Triangle Mesh Protein Docking 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Chang Ha Lee
    • 1
  • Amitabh Varshney
    • 1
  1. 1.Department of Computer Science and UMIACSUniversity of MarylandCollege ParkUSA

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