Visual Support for the Loop Grafting Workflow on Proteins

• Published in: IEEE transactions on visualization and computer graphics 2025-01, Vol.31 (1), p.580-590
• Main Authors: Opaleny, Filip, Ulbrich, Pavol, Planas-Iglesias, Joan, Byska, Jan, Stourac, Jan, Bednar, David, Furmanova, Katarina, Kozlikova, Barbora
• Format: Article
• Language: English
• Subjects: abstract views; Enzymes; Focusing; loop grafting; Pipelines; protein engineering; Protein visualization; Proteins; Shape; Three-dimensional displays; Visualization
• ISSN: 1077-2626; 1941-0506; 1941-0506
• DOI: 10.1109/TVCG.2024.3456401

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.