Twelve Elements of Visualization and Analysis for Tertiary and Quaternary Structure of Biological Molecules

During the last decades, 3D Molecular Graphics in Life Sciences has been used almost exclusively by experts through complex software and applications ranging from Structural Biology to Computer Aided Drug Design. The emergence of JavaScript and WebGL as a viable platform has enabled 3D visualization of biomolecular structures through Web browsers, without any need for specialized software. Although still in its infancy, Web Molecular Graphics opens new perspectives. This white paper, proposes a set of Twelve Elements to consider to enable 3D visualization and structural analyses of biological systems in Web molecular viewers. The Elements go beyond 3D graphics and propose an integrated approach to visualize and analyze molecular entities and their interactions in multiple dimensions, at multiple levels of details, for diverse users. The bridging of 1D sequence browsers and 3D structure viewers, possible under a Web browser, enables information flow where molecular biologists can use structural information directly at the sequence level. Given the tsunami of sequence information linked to diseases from next generation sequencing in need for interpretation making structural information readily available to research scientists is a tremendous opportunity for medical discovery. The Twelve Elements are conceptual and are intended to entice developers to architect software components and APIs, and to gather together as a community around common goals and open source software. A few features of emerging viewers, all available as open source, are highlighted. Speed and quality of 3D graphics for large molecular systems, the interoperability of Web components, and the instantaneous sharing of annotated visualizations through the Web, are some of the most amazing and promising capabilities of 3D Web viewing, opening bright perspectives for Life Sciences research.