New Technique for Representing 3-D Molecular Structures in 2-D Electronic Publications

Published by Berlin Scientists in Latest Issue of TiBS

№ 262/2008 from Sep 08, 2008

A German-Indian group of researchers headed by the immunogeneticist Prof. Dr. Andreas Ziegler of Charité – Universitätsmedizin Berlin and Freie Universität Berlin has developed a technique for integrating illustrative and interactive three-dimensional images of complex structures directly into electronic publications. Using 3-D structural data from the Protein Data Bank (PDB), they showed how 3-D models of molecules can be embedded in the portable document format (PDF). Readers can work with the 3-D models in PDF files without any additional programs. This innovative interactive presentation is particularly  useful for educational purposes. The results were published in the September issue of the journal Trends in Biochemical Sciences (TiBS). The work was supported by the Volkswagen Foundation.

For centuries authors of scientific texts have had to be satisfied with two-dimensional images although they usually describe three-dimensional objects. This is true of biologists and medical researchers as well as geographers and astronomers. Anatomists and geographers have long used three-dimensional objects for educational purposes, but until recently, it was not possible to integrate them into standard texts. This newly developed technique makes it possible for readers to use the materials without constantly being online.

Three-dimensional images can now be integrated in two-dimensional electronic documents using a combination of programs making it possible to embed such objects in PDF documents. The embedded images will appear to be three dimensional and are interactive. The only thing readers need is the ability to access PDF files. The procedure developed by the researchers is documented in TiBS.


  • Kumar, P., Ziegler, A., Ziegler, J., Uchanska-Ziegler, B., and Ziegler, A.: Grasping molecular structures through publication-integrated 3D models. Trends in Biochemical Sciences Vol. 33(9), 408-412 (2008)
  • Tyzack, J.: Dragging (and zooming and rotating) publication of 3D molecular structures into the 21st century. Trends in Biochemical Sciences, Vol. 33(9), 405-407 (2008) (editorial)


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