The University of Utah is awarded a grant to develop new software tools that will allow researchers to create and share accurate and dynamic visual molecular models of molecular processes. As we gain a deeper understanding of the complexity and dynamics of molecular mechanisms, the need for modeling tools that will synthesize diverse molecular and cellular data becomes more urgent. 3D animation software offers an attractive solution to this need, but has been adopted by only a small number of researchers due to the steep learning curve for most 3D graphics applications. This project seeks to enable researchers to create dynamic visualizations of the molecular processes they study, and to share these visualizations with others in the research and educational communities. The Molecular ViewBook project is broken into two major components. First, the 3D Molecular Toolkit, a suite of free software tools that will allow users to start creating molecular animations in an open-source animation software package after viewing a short tutorial. The 3D Molecular Toolkit will include modules that cover all aspects of molecular animation, including easy-to-use tools to import and manipulate structural data, create conformational changes in protein models, and dynamically build higher-order molecular structures. The second component is the Molecular ViewBook website (, a portal which will enable users to share their animations and animation source codes with others. From the Molecular ViewBook website, users can search for molecular animations that other users have created, and modify these animations to add new components.

Molecular animations are increasingly recognized and utilized as a powerful means to communicate complex molecular mechanisms to a wide variety of audiences. In the past several years, we have witnessed a large and rapidly growing interest amongst researchers to be able to create animations. To aid in the dissemination of the Molecular ViewBook, these investigators will conduct local and national workshops for researchers. They will also introduce an Educational Portal that will target biology educators and students at the high school and college levels, thereby expanding our user community beyond the scope of the research community.

Project Report

The goal of the Molecular Flipbook project was to create an intuitive molecular visualization software and online database that would allow biology researchers to more readily create dynamic models of molecular processes. We feel that creating more accurate models of molecular complexes and interactions is absolutely crucial to better explore, understand, communicate and teach molecular biology. The project has two major components: (1) the Molecular Flipbook animation toolkit and (2) the Molecular Flipbook website. The Molecular Flipbook animation toolkit is a novel 3d animation software that was designed specifically for the modeling and animation of molecules. It features an intuitive slide-based animation tool, an import module to animate molecular structures from the Protein Data Bank, modules to change the representation and appearance of molecules, a module to model proteins of unknown structure, and the ability to export animations as a movie file which can then be readily viewed and shared. We have paid particular attention to designing the user interface to be as easy-to-learn as possible, allowing users to readily change their perspective and to move and rotate proteins as needed. Based on our user testing, we have found that researchers with no prior experience with animation software were able to create their first molecular animation after viewing a short video tutorial. The Molecular Flipbook website ( is the online home of Molecular Flipbook, allowing visitors to download the animation toolkit (which is free), view video tutorials, upload their own content to share with others (after creating an account), browse and search the Molecular Flipbook online library, and read news and frequently asked questions about Molecular Flipbook. The library hosts a number of different file types, such as image files and vector illustration files, in addition to 3d animation scene files. The first public version of the Molecular Flipbook animation toolkit was released in the spring of 2014, and the website/database ( was launched in the summer of 2014. Since its launch, the website has received over 13,000 unique visitors.

National Science Foundation (NSF)
Division of Biological Infrastructure (DBI)
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Program Officer
Anne Maglia
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University of Utah
Salt Lake City
United States
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