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Determination and visualization of a protein as a RIN provides insights on the topological properties (and hence their related biological functions) of large proteins without dealing with the full complexity of the three-dimensional description, and hence it represents an invaluable tool of modern bioinformatics.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We present RIN<jats:italic>maker<\/jats:italic>, a fast, flexible, and powerful tool for determining and visualizing RINs that include all standard non-covalent interactions. RIN<jats:italic>maker<\/jats:italic>is offered as a cross-platform and open source software that can be used either as a command-line tool or through a web application or a web API service. We benchmark its efficiency against the main alternatives and provide explicit tests to show its performance and its correctness.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>RIN<jats:italic>maker<\/jats:italic>is designed to be fully customizable, from a simple and handy support for experimental research to a sophisticated computational tool that can be embedded into a large computational pipeline. Hence, it paves the way to bridge the gap between data-driven\/machine learning approaches and numerical simulations of simple, physically motivated, models.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12859-023-05466-y","type":"journal-article","created":{"date-parts":[[2023,9,11]],"date-time":"2023-09-11T17:01:57Z","timestamp":1694451717000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Rinmaker: a fast, versatile and reliable tool to determine residue interaction networks in proteins"],"prefix":"10.1186","volume":"24","author":[{"given":"Alvise","family":"Span\u00f2","sequence":"first","affiliation":[]},{"given":"Lorenzo","family":"Fanton","sequence":"additional","affiliation":[]},{"given":"Davide","family":"Pizzolato","sequence":"additional","affiliation":[]},{"given":"Jacopo","family":"Moi","sequence":"additional","affiliation":[]},{"given":"Francesco","family":"Vinci","sequence":"additional","affiliation":[]},{"given":"Alberto","family":"Pesce","sequence":"additional","affiliation":[]},{"given":"Cedrix J.","family":"Dongmo Foumthuim","sequence":"additional","affiliation":[]},{"given":"Achille","family":"Giacometti","sequence":"additional","affiliation":[]},{"given":"Marta","family":"Simeoni","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,9,11]]},"reference":[{"issue":"7873","key":"5466_CR1","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","volume":"596","author":"J Jumper","year":"2021","unstructured":"Jumper J, Evans R, Pritzel A, et al. 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