{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,2]],"date-time":"2025-11-02T19:58:46Z","timestamp":1762113526214},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Structure of most proteins is flexible. Identification and analysis of intramolecular motions is a complex problem. Breaking a structure into relatively rigid parts, the so-called dynamic domains, may help comprehend the complexity of protein\u2019s mobility. We propose a new approach called ResiCon (Residue Contacts analysis), which performs this task by applying a data-mining analysis of an ensemble of protein configurations and recognizes dynamic domains, hinges and interfacial regions, by considering contacts between residues.<\/jats:p><jats:p>Results: Dynamic domains found by ResiCon are more compact than those identified by two other popular methods: PiSQRD and GeoStaS. The current analysis was carried out using a known reference set of 30 NMR protein structures, as well as molecular dynamics simulation data of flap opening events in HIV-1 protease. The more detailed analysis of HIV-1 protease dataset shows that ResiCon identified dynamic domains involved in structural changes of functional importance.<\/jats:p><jats:p>Availability and implementation: The ResiCon server is available at URL: http:\/\/dworkowa.imdik.pan.pl\/EP\/ResiCon.<\/jats:p><jats:p>Contact: \u00a0pawel@bioexploratorium.pl<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv525","type":"journal-article","created":{"date-parts":[[2015,9,6]],"date-time":"2015-09-06T00:18:10Z","timestamp":1441498690000},"page":"25-34","source":"Crossref","is-referenced-by-count":10,"title":["ResiCon: a method for the identification of dynamic domains, hinges and interfacial regions in proteins"],"prefix":"10.1093","volume":"32","author":[{"given":"Maciej","family":"Dziubi\u0144ski","sequence":"first","affiliation":[{"name":"1 Department of Biophysics and CoE BioExploratorium, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland and"}]},{"given":"Pawe\u0142","family":"Daniluk","sequence":"additional","affiliation":[{"name":"1 Department of Biophysics and CoE BioExploratorium, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland and"},{"name":"2 Bioinformatics Laboratory, Mossakowski Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland"}]},{"given":"Bogdan","family":"Lesyng","sequence":"additional","affiliation":[{"name":"1 Department of Biophysics and CoE BioExploratorium, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland and"},{"name":"2 Bioinformatics Laboratory, Mossakowski Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland"}]}],"member":"286","published-online":{"date-parts":[[2015,9,5]]},"reference":[{"key":"2023020110213980300_btv525-B1","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1016\/S1359-0278(97)00024-2","article-title":"Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential","volume":"2","author":"Bahar","year":"1997","journal-title":"Fold. 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