Midlik Adam, Bittrich Sebastian, Fleming Jennifer R, Nair Sreenath, Velankar Sameer, Burley Stephen K, Young Jasmine Y, Vallat Brinda, Sehnal David
Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom.
Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, United States.
Nucleic Acids Res. 2025 Jul 7;53(W1):W408-W414. doi: 10.1093/nar/gkaf370.
Data visualization is a pivotal component of a structural biologist's arsenal. The Mol* Viewer makes molecular visualizations available to broader audiences via most web browsers. While Mol* provides a wide range of functionality, it has a steep learning curve and is only available via a JavaScript interface. To enhance the accessibility and usability of web-based molecular visualization, we introduce MolViewSpec (molstar.org/mol-view-spec), a standardized approach for defining molecular visualizations that decouples the definition of complex molecular scenes from their rendering. Scene definition can include references to commonly used structural, volumetric, and annotation data formats together with a description of how the data should be visualized and paired with optional annotations specifying colors, labels, measurements, and custom 3D geometries. Developed as an open standard, this solution paves the way for broader interoperability and support across different programming languages and molecular viewers, enabling more streamlined, standardized, and reproducible visual molecular analyses. MolViewSpec is freely available as a Mol* extension and a standalone Python package.
数据可视化是结构生物学家工具库中的关键组成部分。Mol* Viewer通过大多数网络浏览器使分子可视化可供更广泛的受众使用。虽然Mol提供了广泛的功能，但它的学习曲线较陡，并且仅通过JavaScript接口可用。为了提高基于网络的分子可视化的可访问性和可用性，我们引入了MolViewSpec（molstar.org/mol-view-spec），这是一种定义分子可视化的标准化方法，它将复杂分子场景的定义与其渲染解耦。场景定义可以包括对常用结构、体积和注释数据格式的引用，以及对数据应如何可视化以及与指定颜色、标签、测量和自定义3D几何形状的可选注释配对的描述。作为一种开放标准开发，该解决方案为跨不同编程语言和分子查看器的更广泛互操作性和支持铺平了道路，实现了更简化、标准化和可重复的可视化分子分析。MolViewSpec作为Mol扩展和独立的Python包免费提供。
