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Visualization of macromolecular structures

Nature Methods volume 7, pages S42–S55 (2010)Cite this article

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Abstract

Structural biology is rapidly accumulating a wealth of detailed information about protein function, binding sites, RNA, large assemblies and molecular motions. These data are increasingly of interest to a broader community of life scientists, not just structural experts. Visualization is a primary means for accessing and using these data, yet visualization is also a stumbling block that prevents many life scientists from benefiting from three-dimensional structural data. In this review, we focus on key biological questions where visualizing three-dimensional structures can provide insight and describe available methods and tools.

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Figure 1: Visualizing a tyrosine kinase structure (PDB 1QCF)97.
Figure 2: Caution for beginners: symmetry in crystal structures.
Figure 3: Visualization of an NMR ensemble for SH3 (ref. 108).
Figure 4: Visualizing ligand-binding sites.
Figure 5: Visualization of RNA structure in one, two and three dimensions.
Figure 6: Visualizations of molecular motion.
Figure 7: Two examples of multiscale, hierarchical visualization.
Figure 8: Tangible models in research.

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Acknowledgements

Thanks to M. Berynskyy and L. Biedermannova for assistance with Figure 6. This work was partly supported by the European Union Framework Programme 6 grant 'TAMAHUD' (LSHC-CT-2007-037472). R.C.W. gratefully acknowledges the support of the Klaus Tschira Foundation.

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Authors and Affiliations

  1. European Molecular Biology Laboratory, Heidelberg, Germany

    Seán I O'Donoghue & Andrea Schafferhans

  2. The Scripps Research Institute, La Jolla, California, USA

    David S Goodsell & Arthur J Olson

  3. Goethe University, Frankfurt, Germany

    Achilleas S Frangakis

  4. Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, Strasbourg, France

    Fabrice Jossinet & Eric Westhof

  5. European Bioinformatics Institute, Cambridge, UK

    Roman A Laskowski

  6. Institut Pasteur, Paris, France

    Michael Nilges

  7. Institute of Structural and Molecular Biology, Birkbeck College, London, UK

    Helen R Saibil

  8. Heidelberg Institute for Theoretical Sciences (HITS), Heidelberg, Germany

    Rebecca C Wade

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  1. Seán I O'Donoghue
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  2. David S Goodsell
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Correspondence to Seán I O'Donoghue.

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O'Donoghue, S., Goodsell, D., Frangakis, A. et al. Visualization of macromolecular structures. Nat Methods 7 (Suppl 3), S42–S55 (2010). https://doi.org/10.1038/nmeth.1427

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