{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T15:24:05Z","timestamp":1764689045156},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":480,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Biological molecules perform their functions through interactions with other molecules. Structure alignment of interaction interfaces between biological complexes is an indispensable step in detecting their structural similarities, which are keys to understanding their evolutionary histories and functions. Although various structure alignment methods have been developed to successfully access the similarities of protein structures or certain types of interaction interfaces, existing alignment tools cannot directly align arbitrary types of interfaces formed by protein, DNA or RNA molecules. Specifically, they require a \u2018blackbox preprocessing\u2019 to standardize interface types and chain identifiers. Yet their performance is limited and sometimes unsatisfactory.<\/jats:p><jats:p>Results: Here we introduce a novel method, PROSTA-inter, that automatically determines and aligns interaction interfaces between two arbitrary types of complex structures. Our method uses sequentially remote fragments to search for the optimal superimposition. The optimal residue matching problem is then formulated as a maximum weighted bipartite matching problem to detect the optimal sequence order-independent alignment. Benchmark evaluation on all non-redundant protein\u2013DNA complexes in PDB shows significant performance improvement of our method over TM-align and iAlign (with the \u2018blackbox preprocessing\u2019). Two case studies where our method discovers, for the first time, structural similarities between two pairs of functionally related protein\u2013DNA complexes are presented. We further demonstrate the power of our method on detecting structural similarities between a protein\u2013protein complex and a protein\u2013RNA complex, which is biologically known as a protein\u2013RNA mimicry case.<\/jats:p><jats:p>Availability and implementation: The PROSTA-inter web-server is publicly available at http:\/\/www.cbrc.kaust.edu.sa\/prosta\/.<\/jats:p><jats:p>Contact: \u00a0xin.gao@kaust.edu.sa<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv242","type":"journal-article","created":{"date-parts":[[2015,6,13]],"date-time":"2015-06-13T17:12:36Z","timestamp":1434215556000},"page":"i133-i141","source":"Crossref","is-referenced-by-count":19,"title":["Finding optimal interaction interface alignments between biological complexes"],"prefix":"10.1093","volume":"31","author":[{"given":"Xuefeng","family":"Cui","sequence":"first","affiliation":[{"name":"Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia"}]},{"given":"Hammad","family":"Naveed","sequence":"additional","affiliation":[{"name":"Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia"}]},{"given":"Xin","family":"Gao","sequence":"additional","affiliation":[{"name":"Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia"}]}],"member":"286","published-online":{"date-parts":[[2015,6,10]]},"reference":[{"key":"2023020115433794500_btv242-B1","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1042\/BJ20140298","article-title":"How to find a leucine in a haystack? 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