Visualization of Macromolecular Structures

European Molecular Biology Laboratory, Heidelberg, Germany.
Nature Methods (Impact Factor: 32.07). 03/2010; 7(3 Suppl):S42-55. DOI: 10.1038/nmeth.1427
Source: PubMed


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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Available from: Roman Aleksander Laskowski, Mar 11, 2014
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    • "Cytoscape visualizes the information as a twodimensional figure of the network, and the visual properties of the nodes/edges can be customized according to their parameters . To visualize molecular structures, the scholar can select from many available molecular viewers (for a review of these, see O'Donoghue et al., 2010). Molecular viewers are sophisticated software tools that not only highlight particular aspects of one or many molecules/proteins but can also analyze the Structure 23, 1–8, May 5, 2015 ª2015 Elsevier Ltd All rights reserved 1 "
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    ABSTRACT: It can be informative to view biological data, e.g., protein-protein interactions within a large complex, in a network representation coupled with three-dimensional structural visualizations of individual molecular entities. CyToStruct, introduced here, provides a transparent interface between the Cytoscape platform for network analysis and molecular viewers, including PyMOL, UCSF Chimera, VMD, and Jmol. CyToStruct launches and passes scripts to molecular viewers from the network's edges and nodes. We provide demonstrations to analyze interactions among subunits in large protein/RNA/DNA complexes, and similarities among proteins. CyToStruct enriches the network tools of Cytoscape by adding a layer of structural analysis, offering all capabilities implemented in molecular viewers. CyToStruct is available at and in the Cytoscape App Store. Given the coordinates of a molecular complex, our web server ( automatically generates all files needed to visualize the complex as a Cytoscape network with CyToStruct bridging to PyMOL, UCSF Chimera, VMD, and Jmol. Copyright © 2015 Elsevier Ltd. All rights reserved.
    Structure 04/2015; 23(5). DOI:10.1016/j.str.2015.02.013 · 5.62 Impact Factor
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    • "However, our virtual modeling system differed from concrete models in that the shape of the hand-held interface and the viewed object were not congruent. This contrasts with earlier work in our laboratory (Keehner et al., 2008) in which the shape of the interface and model were the same (both were simple egg-shaped solids) or with the work of O'Donoghue et al. (2010), who have developed hybrid virtual models that use augmented reality to incorporate a high fidelity haptic interface (that has the same shape as the viewed model) with a detailed virtual image based on the intuition that there is a benefit of both haptic cues and virtual images. A second difference was that our virtual models had limited interactivity, which allowed students to only rotate the model around the central carbon–carbon bond, whereas all bonds could be rotated on the concrete models. "
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    ABSTRACT: Virtual models are increasingly common in the modern science classroom, however little is known about the relative effectiveness of virtual and concrete models. We developed a virtual modeling system and tested the benefit of haptic cue fidelity, controlling for many other perceptual differences between concrete and virtual models. In two studies we directly compared performance of students using this virtual model and using concrete models for tasks in the domain of organic chemistry. Students used either virtual or concrete models to match diagrams of molecules or compare the structures of molecules represented by models and diagrams. The results indicated similar levels of accuracy and similar ratings of usability for virtual and concrete models but no effect of haptic cue fidelity. Greater efficiency with virtual models was observed when students matched diagrams and models, and this efficiency transferred to later use of concrete models. The efficiency benefit is attributed to interactive constraints of the hand-held interface to the virtual model, which helped students identify task-relevant information in the model and limited them to performing the most task-relevant interactions with the models.
    Computers in Human Behavior 11/2013; 29(6):2546-2556. DOI:10.1016/j.chb.2013.06.012 · 2.69 Impact Factor
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    • "Biology currently undergoes a rapid expansion, calling for tools to visualize huge and complex systems, such as macromolecular structures, -omics networks or even organs and organisms [1]–[3]. It is a particular challenge for academic researchers to develop software solutions meeting these demands. "
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    ABSTRACT: The video games industry develops ever more advanced technologies to improve rendering, image quality, ergonomics and user experience of their creations providing very simple to use tools to design new games. In the molecular sciences, only a small number of experts with specialized know-how are able to design interactive visualization applications, typically static computer programs that cannot easily be modified. Are there lessons to be learned from video games? Could their technology help us explore new molecular graphics ideas and render graphics developments accessible to non-specialists? This approach points to an extension of open computer programs, not only providing access to the source code, but also delivering an easily modifiable and extensible scientific research tool. In this work, we will explore these questions using the Unity3D game engine to develop and prototype a biological network and molecular visualization application for subsequent use in research or education. We have compared several routines to represent spheres and links between them, using either built-in Unity3D features or our own implementation. These developments resulted in a stand-alone viewer capable of displaying molecular structures, surfaces, animated electrostatic field lines and biological networks with powerful, artistic and illustrative rendering methods. We consider this work as a proof of principle demonstrating that the functionalities of classical viewers and more advanced novel features could be implemented in substantially less time and with less development effort. Our prototype is easily modifiable and extensible and may serve others as starting point and platform for their developments. A webserver example, standalone versions for MacOS X, Linux and Windows, source code, screen shots, videos and documentation are available at the address:
    PLoS ONE 03/2013; 8(3):e57990. DOI:10.1371/journal.pone.0057990 · 3.23 Impact Factor
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