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Interactive Analysis and Visualization of Macromolecular Interfaces between Proteins

  • Marco Wiltgen
  • Andreas Holzinger
  • Gernot P. Tilz
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4799)

Abstract

Molecular interfaces between proteins are of high importance for understanding their interactions and functions. In this paper protein complexes in the PDB database are used as input to calculate an interface contact matrix between two proteins, based on the distance between individual residues and atoms of each protein. The interface contact matrix is linked to a 3D visualization of the macromolecular structures in that way, that mouse clicking on the appropriate part of the interface contact matrix highlights the corresponding residues in the 3D structure. Additionally, the identified residues in the interface contact matrix are used to define the molecular surface at the interface. The interface contact matrix allows the end user to overview the distribution of the involved residues and an evaluation of interfacial binding hot spots. Theinteractive visualization of the selected residues in a 3D view via interacting windows allows realistic analysis of the macromolecular interface.

Keywords

Interface Contact Matrix Bioinformatics Macromolecular Interfaces Human–Computer Interaction Tumour Necrosis Factor 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Marco Wiltgen
    • 1
  • Andreas Holzinger
    • 1
  • Gernot P. Tilz
    • 2
  1. 1.Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, A-8036 GrazAustria
  2. 2.Centre d’Etude du Polymorphysme Humain, 27 rue Juliette Dadu, F-75010 ParisFrance

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