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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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability<\/jats:title>\n                    <jats:p>\n                      GitHub (\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/github.com\/t03i\/FlatProt\" ext-link-type=\"uri\">https:\/\/github.com\/t03i\/FlatProt<\/jats:ext-link>\n                      ); Zenodo (\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/doi.org\/10.5281\/zenodo.15697296\" ext-link-type=\"uri\">https:\/\/doi.org\/10.5281\/zenodo.15697296<\/jats:ext-link>\n                      ).\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-025-06233-x","type":"journal-article","created":{"date-parts":[[2025,8,13]],"date-time":"2025-08-13T06:11:49Z","timestamp":1755065509000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["FlatProt: 2D visualization eases protein structure comparison"],"prefix":"10.1186","volume":"26","author":[{"given":"Tobias","family":"Olenyi","sequence":"first","affiliation":[]},{"given":"Constantin","family":"Carl","sequence":"additional","affiliation":[]},{"given":"Tobias","family":"Senoner","sequence":"additional","affiliation":[]},{"given":"Ivan","family":"Koludarov","sequence":"additional","affiliation":[]},{"given":"Burkhard","family":"Rost","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2025,8,13]]},"reference":[{"issue":"3","key":"6233_CR1","doi-asserted-by":"publisher","first-page":"4849","DOI":"10.1109\/TNNLS.2024.3359657","volume":"36","author":"Q Lv","year":"2025","unstructured":"Lv Q, Chen G, Yang Z, Zhong W, Chen CY. 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After using these services, the authors reviewed and edited the content as needed and take full responsibility for the content of the published article.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Generative AI and AI-assisted technologies in the writing process"}},{"value":"The authors declare no competing interests.","order":5,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"210"}}