{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,20]],"date-time":"2025-09-20T19:02:44Z","timestamp":1758394964721},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation The remodeling of short fragment(s) of the protein backbone to accommodate new function(s), fine-tune binding specificities or change\/create novel protein interactions is a common task in structure-based computational design. Alternative backbone conformations can be generated de novo or by redeploying existing fragments extracted from protein structures i.e. knowledge-based. We present Frag\u2019r\u2019Us, a web server designed to sample alternative protein backbone conformations in loop regions. The method relies on a database of super secondary structural motifs called s motifs. Thus, sampling of conformations reflects structurally feasible fragments compiled from existing protein structures.<\/jats:p>\n               <jats:p>Availability and implementation Frag\u2019r\u2019Us has been implemented as web application and is available at http:\/\/www.bioinsilico.org\/FRAGRUS .<\/jats:p>\n               <jats:p>Contact \u00a0narcis.fernandez@gmail.com or baldo.oliva@upf.edu<\/jats:p>\n               <jats:p>Supplementary information \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu129","type":"journal-article","created":{"date-parts":[[2014,3,7]],"date-time":"2014-03-07T02:57:42Z","timestamp":1394161062000},"page":"1935-1936","source":"Crossref","is-referenced-by-count":19,"title":["Frag\u2019r\u2019Us: knowledge-based sampling of protein backbone conformations for \n            <i>de novo<\/i>\n             structure-based protein design"],"prefix":"10.1093","volume":"30","author":[{"given":"Jaume","family":"Bonet","sequence":"first","affiliation":[{"name":"1 Structural Bioinformatics Lab (GRIB), Universitat Pompeu Fabra, Barcelona, Catalonia 08003, Spain, 2 Department of Structure of Macromolecules, CNB-CSIC, Cantoblanco, 28049 Madrid, Spain and 3 Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, SY23 3DA Ceredigion, UK"}]},{"given":"Joan","family":"Segura","sequence":"additional","affiliation":[{"name":"1 Structural Bioinformatics Lab (GRIB), Universitat Pompeu Fabra, Barcelona, Catalonia 08003, Spain, 2 Department of Structure of Macromolecules, CNB-CSIC, Cantoblanco, 28049 Madrid, Spain and 3 Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, SY23 3DA Ceredigion, UK"}]},{"given":"Joan","family":"Planas-Iglesias","sequence":"additional","affiliation":[{"name":"1 Structural Bioinformatics Lab (GRIB), Universitat Pompeu Fabra, Barcelona, Catalonia 08003, Spain, 2 Department of Structure of Macromolecules, CNB-CSIC, Cantoblanco, 28049 Madrid, Spain and 3 Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, SY23 3DA Ceredigion, UK"}]},{"given":"Baldomero","family":"Oliva","sequence":"additional","affiliation":[{"name":"1 Structural Bioinformatics Lab (GRIB), Universitat Pompeu Fabra, Barcelona, Catalonia 08003, Spain, 2 Department of Structure of Macromolecules, CNB-CSIC, Cantoblanco, 28049 Madrid, Spain and 3 Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, SY23 3DA Ceredigion, UK"}]},{"given":"Narcis","family":"Fernandez-Fuentes","sequence":"additional","affiliation":[{"name":"1 Structural Bioinformatics Lab (GRIB), Universitat Pompeu Fabra, Barcelona, Catalonia 08003, Spain, 2 Department of Structure of Macromolecules, CNB-CSIC, Cantoblanco, 28049 Madrid, Spain and 3 Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, SY23 3DA Ceredigion, UK"}]}],"member":"286","published-online":{"date-parts":[[2014,3,6]]},"reference":[{"key":"2023012711181868300_btu129-B1","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1126\/science.1209368","article-title":"Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold","volume":"334","author":"Azoitei","year":"2011","journal-title":"Science"},{"key":"2023012711181868300_btu129-B2","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1038\/80734","article-title":"The Protein Data Bank and the challenge of structural genomics","volume":"7","author":"Berman","year":"2000","journal-title":"Nat. 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