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Computational design, fabrication and evaluation of rubber protein models
Computers & Graphics ( IF 2.5 ) Pub Date : 2021-06-06 , DOI: 10.1016/j.cag.2021.05.010
Thomas Alderighi , Daniela Giorgi , Luigi Malomo , Paolo Cignoni , Monica Zoppè

Tangible 3D molecular models conceptualize complex phenomena in a stimulating and engaging format. This is especially true for learning environments, where additive manufacturing is increasingly used to produce teaching aids for chemical education. However, the 3D models presented previously are limited in the type of molecules they can represent and the amount of information they carry. In addition, they have little role in representing complex biological entities such as proteins. We present the first complete workflow for the fabrication of soft models of complex proteins of any size. We leverage on molding technologies to generate accurate, soft models which incorporate both spatial and functional aspects of large molecules. Our method covers the whole pipeline from molecular surface preparation and editing to actual 3D model fabrication. The models fabricated with our strategy can be used as aids to illustrate biological functional behavior, such as assembly in quaternary structure and docking mechanisms, which are difficult to convey with traditional visualization methods. We applied the proposed framework to fabricate a set of 3D protein models, and we validated the appeal of our approach in a classroom setting.



中文翻译:

橡胶蛋白模型的计算设计、制作和评估

有形的 3D 分子模型以刺激和引人入胜的形式将复杂现象概念化。对于学习环境来说尤其如此,在这种环境中,增材制造越来越多地用于生产化学教育的教具。然而,之前介绍的 3D 模型在它们可以表示的分子类型和它们携带的信息量方面受到限制。此外,它们在表示复杂的生物实体(如蛋白质)方面几乎没有作用。我们展示了第一个完整的工作流程,用于制造任何大小的复杂蛋白质的软模型。我们利用成型技术来生成准确的软模型,这些模型结合了大分子的空间和功能方面。我们的方法涵盖了从分子表面制备和编辑到实际 3D 模型制造的整个流程。使用我们的策略构建的模型可以用作说明生物功能行为的辅助工具,例如四级结构中的组装和对接机制,这些是传统可视化方法难以传达的。我们应用所提出的框架来制作一组 3D 蛋白质模型,并验证了我们的方法在课堂环境中的吸引力。

更新日期:2021-06-24
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