FlatProt: 2D visualization eases protein structure comparison
Abstract Background Understanding and comparing three-dimensional (3D) structures of proteins can advance bioinformatics, molecular biology, and drug discovery. While 3D models offer detailed insights, comparing multiple structures simultaneously remains challenging, especially on two-dimensional (2...
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| Format: | Article |
| Language: | English |
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BMC
2025-08-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-025-06233-x |
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| author | Tobias Olenyi Constantin Carl Tobias Senoner Ivan Koludarov Burkhard Rost |
| author_facet | Tobias Olenyi Constantin Carl Tobias Senoner Ivan Koludarov Burkhard Rost |
| author_sort | Tobias Olenyi |
| collection | DOAJ |
| description | Abstract Background Understanding and comparing three-dimensional (3D) structures of proteins can advance bioinformatics, molecular biology, and drug discovery. While 3D models offer detailed insights, comparing multiple structures simultaneously remains challenging, especially on two-dimensional (2D) displays. Existing 2D visualization tools lack standardized approaches for pipelined inspection of large protein sets, limiting their utility in large-scale pre-filtering. Results We introduce FlatProt, a tool designed to complement 3D viewers by enabling standardized 2D visualization of individual protein structures or large sets thereof. By including Foldseek-based family rotation alignment or an inertia-based fallback, FlatProt creates consistent and scalable visual representations for user-defined protein structures. It supports domain-aware decomposition, family-level overlays, and lightweight visual abstraction of secondary structures. FlatProt processes proteins efficiently, as showcased on a subset of the human-proteome. Conclusion FlatProt provides clear, consistent, user-friendly visualizations that support rapid, comparative inspection of protein structures at scale. By bridging the gap between interactive 3D tools and static visual summaries, it enables users to explore conserved features, detect outliers, and prioritize structures for further analysis. Availability GitHub ( https://github.com/t03i/FlatProt ); Zenodo ( https://doi.org/10.5281/zenodo.15697296 ). |
| format | Article |
| id | doaj-art-232e3b336af0428f9d1070a4f7ac4da1 |
| institution | Kabale University |
| issn | 1471-2105 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj-art-232e3b336af0428f9d1070a4f7ac4da12025-08-20T04:02:45ZengBMCBMC Bioinformatics1471-21052025-08-0126111310.1186/s12859-025-06233-xFlatProt: 2D visualization eases protein structure comparisonTobias Olenyi0Constantin Carl1Tobias Senoner2Ivan Koludarov3Burkhard Rost4Department of Informatics, Bioinformatics & Computational Biology, School of Computation, Information, and Technology (CIT), TUM (Technical University of Munich)Department of Informatics, Bioinformatics & Computational Biology, School of Computation, Information, and Technology (CIT), TUM (Technical University of Munich)Department of Informatics, Bioinformatics & Computational Biology, School of Computation, Information, and Technology (CIT), TUM (Technical University of Munich)Department of Informatics, Bioinformatics & Computational Biology, School of Computation, Information, and Technology (CIT), TUM (Technical University of Munich)Department of Informatics, Bioinformatics & Computational Biology, School of Computation, Information, and Technology (CIT), TUM (Technical University of Munich)Abstract Background Understanding and comparing three-dimensional (3D) structures of proteins can advance bioinformatics, molecular biology, and drug discovery. While 3D models offer detailed insights, comparing multiple structures simultaneously remains challenging, especially on two-dimensional (2D) displays. Existing 2D visualization tools lack standardized approaches for pipelined inspection of large protein sets, limiting their utility in large-scale pre-filtering. Results We introduce FlatProt, a tool designed to complement 3D viewers by enabling standardized 2D visualization of individual protein structures or large sets thereof. By including Foldseek-based family rotation alignment or an inertia-based fallback, FlatProt creates consistent and scalable visual representations for user-defined protein structures. It supports domain-aware decomposition, family-level overlays, and lightweight visual abstraction of secondary structures. FlatProt processes proteins efficiently, as showcased on a subset of the human-proteome. Conclusion FlatProt provides clear, consistent, user-friendly visualizations that support rapid, comparative inspection of protein structures at scale. By bridging the gap between interactive 3D tools and static visual summaries, it enables users to explore conserved features, detect outliers, and prioritize structures for further analysis. Availability GitHub ( https://github.com/t03i/FlatProt ); Zenodo ( https://doi.org/10.5281/zenodo.15697296 ).https://doi.org/10.1186/s12859-025-06233-xProtein visualizationBioinformatics toolsProtein structureSequence comparison |
| spellingShingle | Tobias Olenyi Constantin Carl Tobias Senoner Ivan Koludarov Burkhard Rost FlatProt: 2D visualization eases protein structure comparison BMC Bioinformatics Protein visualization Bioinformatics tools Protein structure Sequence comparison |
| title | FlatProt: 2D visualization eases protein structure comparison |
| title_full | FlatProt: 2D visualization eases protein structure comparison |
| title_fullStr | FlatProt: 2D visualization eases protein structure comparison |
| title_full_unstemmed | FlatProt: 2D visualization eases protein structure comparison |
| title_short | FlatProt: 2D visualization eases protein structure comparison |
| title_sort | flatprot 2d visualization eases protein structure comparison |
| topic | Protein visualization Bioinformatics tools Protein structure Sequence comparison |
| url | https://doi.org/10.1186/s12859-025-06233-x |
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