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)


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.


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


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Perutz, M.F., Muirhead, H., Cox, J.M., Goaman, L.C.: Three-dimensional Fourier synthesis of horse oxyhaemoglobin at 2.8 angstrom resolution: the atomic model. Nature 219, 131–139 (1968)CrossRefGoogle Scholar
  2. 2.
    Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The Protein Data Bank. Nucleic Acids Research, 28, 235–243 (2000)Google Scholar
  3. 3.
    Lesk, A.M.: Introduction to Bioinformatics. Oxford University Press, Oxford (2002)Google Scholar
  4. 4.
    Gibas, C., Jambeck, P.: Developing Bioinformatics Computer Skills, O’Reilly (2001)Google Scholar
  5. 5.
    Chang, P.L.: Clinical bioinformatics. Chang. Gung. Med. J. 28(4), 201–211 (2005)Google Scholar
  6. 6.
    Mount, D.W.: Bioinformatics: sequence and genome analysis. Cold Spring Harbor laboratory Press, New York (2001)Google Scholar
  7. 7.
    Hogue, C.W.: Cn3D: A new generation of three-dimensional molecular structure viewer. Trends Biochemical Science 22, 314–316 (1997)CrossRefGoogle Scholar
  8. 8.
    Walther, D.: WebMol- a Java based PDB viewer. Trends Biochem Science 22, 274–275 (1997)CrossRefGoogle Scholar
  9. 9.
    Gabdoulline, R.R., Hoffmann, R., Leitner, F., Wade, R.C.: ProSAT: functional annotation of protein 3D structures. Bioinformatics 1,19(13), 1723–1725 (2003)CrossRefGoogle Scholar
  10. 10.
    Neshich, G., Rocchia, W., Mancini, A.L., et al.: Java Protein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure. Nucleic Acids Res. 1,32, 595–601 (2004)CrossRefGoogle Scholar
  11. 11.
    Oldfield, T.J.: A Java applet for multiple linked visualization of protein structure andsequence. J.Comput. Aided. Mol. Des. 18(4), 225–234 (2004)CrossRefGoogle Scholar
  12. 12.
    Wiltgen, M., Holzinger, A.: Visualization in Bioinformatics: Protein Structures with Physicochemical and Biological Annotations. In: Zara, J., Sloup, J. (eds.) CEMVRC 2005. Central European Multimedia and Virtual Reality Conference, pp. 69–74. Eurographics Library (2005)Google Scholar
  13. 13.
    Holzinger, A., Geierhofer, R., Errath, M.: Semantic Information in Medical Information Systems - from Data and Information to Knowledge: Facing Information Overload. In: Proceedings of I-MEDIA 2007 and I-SEMANTICS 2007, pp. 323–330 (2007)Google Scholar
  14. 14.
    Holzinger, A.: Usability Engineering for Software Developers. Communications of the ACM 48(1), 71–74 (2005)CrossRefGoogle Scholar
  15. 15.
    Gabdoulline, R.R., Wade, R.C., Walther, D.: MolSurfer: A macromolecular interface navigator. Nucleid Acids Res. 1,31(13), 3349–3351 (2003)CrossRefGoogle Scholar
  16. 16.
    Finn, R.D., Marshall, M., Bateman, A.: iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics 21(3), 410–412 (2005)CrossRefGoogle Scholar
  17. 17.
    Banner, D.W.,  D‘Arcy, A.,  Janes, W.,  Gentz, R.,  Schoenfeld, H.,  Broger, C.,  Loetscher, H.,  Lesslauer, W.: Crystal structure of the soluble human 55 kd TNF receptor-human TNF beta complex: implications for TNF receptor activation. Cell 73, 431–445 ( 1993)Google Scholar
  18. 18.
    Guex, N., Peitsch, M.C.: SWISS-MODEL and the Swiss-Pdb Viewer: An environment for comparative protein modelling. Electrophoresis 18, 2714–2723 (1997)CrossRefGoogle Scholar
  19. 19.
    Duncan, B., Olson, A.J.: Approximation and characterization of molecular surfaces. Biopolymers 33, 219–229 (1993)CrossRefGoogle Scholar
  20. 20.
    Kim, Y.S., Morgan, M.J., Choksi, S., Liu, Z.G.: TNF-Induced Activation of the Nox1 NADPH Oxidase and Its Role in the Induction of Necrotic Cell Death. Mol. Cell. 8, 26(5), 675–687 (2007)CrossRefGoogle Scholar
  21. 21.
    Vielhauer, V., Mayadas, T.N.: Functions of TNF and its Receptors in Renal Disease: Distinct Roles in Inflammatory Tissue Injury and Immune Regulation. Semin Nephrol. 27(3), 286–308 (2007)CrossRefGoogle Scholar
  22. 22.
    Assi, L.k., Wong, S.H., Ludwig, A., Raga, K., Gordon, C., Salmon, M., Lord, J.M., Scheel-Toellner, D.: Tumor necrosis factor alpha activates release of B lymphocyte stimulator by neutrophils infiltrating the rheumatoid joint. Arthritis Rheum. 56(6), 1776–1786 (2007)CrossRefGoogle Scholar

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

Personalised recommendations