In understanding and redesigning the function of proteins in modern biochemistry, protein engineers are increasingly focusing on exploring regions in proteins called loops. Analyzing various characteristics of these regions helps the experts design the transfer of the desired function from one protein to another. This process is denoted as loop grafting. We designed a set of interactive visualizations that provide experts with visual support through all the loop grafting pipeline steps. The workflow is divided into several phases, reflecting the steps of the pipeline. Each phase is supported by a specific set of abstracted 2D visual representations of proteins and their loops that are interactively linked with the 3D View of proteins. By sequentially passing through the individual phases, the user shapes the list of loops that are potential candidates for loop grafting. Finally, the actual in-silico insertion of the loop candidates from one protein to the other is performed, and the results are visually presented to the user. In this way, the fully computational rational design of proteins and their loops results in newly designed protein structures that can be further assembled and tested through in-vitro experiments. We showcase the contribution of our visual support design on a real case scenario changing the enantiomer selectivity of the engineered enzyme. Moreover, we provide the readers with the experts' feedback.

翻译：在现代生物化学中，为理解和重新设计蛋白质的功能，蛋白质工程师日益聚焦于探索蛋白质中称为环的区域。分析这些区域的各种特征有助于专家设计将所需功能从一个蛋白质转移至另一个蛋白质的过程，该过程被称为环移植。我们设计了一套交互式可视化工具，为专家提供贯穿整个环移植流程各步骤的可视化支持。该工作流程被划分为若干阶段，以对应管线的各个步骤。每个阶段由一组特定的蛋白质及其环的抽象二维可视化表示提供支持，这些二维视图与蛋白质的三维视图实现交互联动。通过依次完成各个阶段，用户可逐步筛选出可能适合进行环移植的候选环列表。最终，系统执行候选环从一个蛋白质到另一个蛋白质的实际计算机模拟插入操作，并将结果可视化呈现给用户。通过这种方式，对蛋白质及其环进行完全基于计算的理性设计，可产生新设计的蛋白质结构，这些结构可通过体外实验进一步组装与测试。我们通过一个实际案例——改变工程化酶的对映体选择性——展示了可视化支持设计的贡献。此外，我们还向读者提供了专家的反馈意见。