{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:50Z","timestamp":1772138090668,"version":"3.50.1"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2018,9,1]],"date-time":"2018-09-01T00:00:00Z","timestamp":1535760000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","award":["2012-5270"],"award-info":[{"award-number":["2012-5270"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","award":["2016-05369"],"award-info":[{"award-number":["2016-05369"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100017156","name":"Swedish e-Science Research Center","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100017156","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Foundation Blanceflor Boncompagni Ludovisi"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Protein\u2013protein interactions (PPI) are essential for the function of the cellular machinery. The rapid growth of protein\u2013protein complexes with known 3D structures offers a unique opportunity to study PPI to gain crucial insights into protein function and the causes of many diseases. In particular, it would be extremely useful to compare interaction surfaces of monomers, as this would enable the pinpointing of potential interaction surfaces based solely on the monomer structure, without the need to predict the complete complex structure. While there are many structural alignment algorithms for individual proteins, very few have been developed for protein interfaces, and none that can align only the interface residues to other interfaces or surfaces of interacting monomer subunits in a topology independent (non-sequential) manner.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present InterComp, a method for topology and sequence-order independent structural comparisons. The method is general and can be applied to various structural comparison applications. By representing residues as independent points in space rather than as a sequence of residues, InterComp can be applied to a wide range of problems including interface\u2013surface comparisons and interface\u2013interface comparisons. We demonstrate a use-case by applying InterComp to find similar protein interfaces on the surface of proteins. We show that InterComp pinpoints the correct interface for almost half of the targets (283 of 586) when considering the top 10 hits, and for 24% of the top 1, even when no templates can be found with regular sequence-order dependent structural alignment methods.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The source code and the datasets are available at: http:\/\/wallnerlab.org\/InterComp.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty587","type":"journal-article","created":{"date-parts":[[2018,7,5]],"date-time":"2018-07-05T21:20:56Z","timestamp":1530825656000},"page":"i787-i794","source":"Crossref","is-referenced-by-count":14,"title":["Topology independent structural matching discovers novel templates for protein interfaces"],"prefix":"10.1093","volume":"34","author":[{"given":"Claudio","family":"Mirabello","sequence":"first","affiliation":[{"name":"Division of Bioinformatics, Department of Physics, Chemistry and Biology, Link\u00f6ping University, Link\u00f6ping SE, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bj\u00f6rn","family":"Wallner","sequence":"additional","affiliation":[{"name":"Division of Bioinformatics, Department of Physics, Chemistry and Biology, Link\u00f6ping University, Link\u00f6ping SE, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,9,8]]},"reference":[{"key":"2023061313500581700_bty587-B1","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1016\/S0092-8674(00)80922-8","article-title":"The cell as a collection of protein machines: preparing the next generation of molecular biologists","volume":"92","author":"Alberts","year":"1998","journal-title":"Cell"},{"key":"2023061313500581700_bty587-B2","doi-asserted-by":"crossref","first-page":"5896","DOI":"10.1073\/pnas.092147999","article-title":"Interrogating protein interaction networks through structural biology","volume":"99","author":"Aloy","year":"2002","journal-title":"Proc. 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