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A Visual Environment for Data Driven Protein Modeling and Validation
Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Swedish e-Science Research Centre (SeRC), Sweden. (Scientific Visualization Group)ORCID iD: 0000-0003-1511-5006
Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.ORCID iD: 0000-0001-8920-017X
Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Swedish e-Science Research Centre (SeRC), Sweden.ORCID iD: 0000-0002-2849-6146
Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Kahlert School of Computing, University of Utah.ORCID iD: 0000-0002-8480-2152
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2023 (English)In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506Article in journal (Refereed) Epub ahead of print
Abstract [en]

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.

Place, publisher, year, edition, pages
Institute of Electrical and Electronics Engineers (IEEE), 2023.
Keywords [en]
molecular visualization, cryo-EM, model validation, verification
National Category
Computer Sciences
Identifiers
URN: urn:nbn:se:liu:diva-195458DOI: 10.1109/tvcg.2023.3286582PubMedID: 37327104OAI: oai:DiVA.org:liu-195458DiVA, id: diva2:1771551
Funder
ELLIIT - The Linköping‐Lund Initiative on IT and Mobile CommunicationsSwedish Research Council, 2015-05462Knut and Alice Wallenberg Foundation, KAW 2019.0024NIH (National Institutes of Health), R01EB023947NIH (National Institutes of Health), R01EB031872
Note

The supplemental material is available under https://osf.io/pqymt/ (DOI: 10.17605/OSF.IO/PQYMT).

Available from: 2023-06-20 Created: 2023-06-20 Last updated: 2024-03-28Bibliographically approved

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Falk, MartinBock, AlexanderHansen, CharlesYnnerman, Anders

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