A Visual Environment for Data Driven Protein Modeling and Validation

• Published in: IEEE transactions on visualization and computer graphics Vol. 30; no. 8; pp. 5063 - 5073
• Main Authors: Falk, Martin, Tobiasson, Victor, Bock, Alexander, Hansen, Charles, Ynnerman, Anders
• Format: Journal Article
• Language: English
• Published: United States IEEE 01.08.2024; The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
• Subjects: Analytical models; Biological system modeling; Computer Graphics; cryo-EM; Cryoelectron Microscopy - methods; Electron microscopes; Image reconstruction; Measurement; model validation; Modelling; Models, Molecular; Molecular visualization; Protein Conformation; Proteins; Proteins - chemistry; Subject specialists; Three-dimensional displays; User-Computer Interface; verification; Visualization
• ISSN: 1077-2626; 1941-0506; 1941-0506
• DOI: 10.1109/TVCG.2023.3286582

In structural biology, validation and verification of new atomic models are crucial and necessary steps which limit the production of reliable molecular models for publications and databases. An atomic model is the result of meticulous modeling and matching and is evaluated using a variety of metrics that provide clues to improve and refine the model so it fits our understanding of molecules and physical constraints. In cryo electron microscopy (cryo-EM) the validation is also part of an iterative modeling process in which there is a need to judge the quality of the model during the creation phase. A shortcoming is that the process and results of the validation are rarely communicated using visual metaphors. This work presents a visual framework for molecular validation. The framework was developed in close collaboration with domain experts in a participatory design process. Its core is a novel visual representation based on 2D heatmaps that shows all available validation metrics in a linear fashion, presenting a global overview of the atomic model and provide domain experts with interactive analysis tools. Additional information stemming from the underlying data, such as a variety of local quality measures, is used to guide the user's attention toward regions of higher relevance. Linked with the heatmap is a three-dimensional molecular visualization providing the spatial context of the structures and chosen metrics. Additional views of statistical properties of the structure are included in the visual framework. We demonstrate the utility of the framework and its visual guidance with examples from cryo-EM.