{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T22:44:00Z","timestamp":1783118640863,"version":"3.54.6"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2017,4,18]],"date-time":"2017-04-18T00:00:00Z","timestamp":1492473600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["AF 1527292"],"award-info":[{"award-number":["AF 1527292"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["DBI 1458509"],"award-info":[{"award-number":["DBI 1458509"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["ERCstG 310873"],"award-info":[{"award-number":["ERCstG 310873"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>We present an approach for the efficient docking of peptide motifs to their free receptor structures. Using a motif based search, we can retrieve structural fragments from the Protein Data Bank (PDB) that are very similar to the peptide\u2019s final, bound conformation. We use a Fast Fourier Transform (FFT) based docking method to quickly perform global rigid body docking of these fragments to the receptor. According to CAPRI peptide docking criteria, an acceptable conformation can often be found among the top-ranking predictions.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>The method is available as part of the protein-protein docking server ClusPro at https:\/\/peptidock.cluspro.org\/nousername.php.<\/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\/btx216","type":"journal-article","created":{"date-parts":[[2017,4,14]],"date-time":"2017-04-14T19:08:51Z","timestamp":1492196931000},"page":"3299-3301","source":"Crossref","is-referenced-by-count":125,"title":["ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT"],"prefix":"10.1093","volume":"33","author":[{"given":"Kathryn A","family":"Porter","sequence":"first","affiliation":[{"name":"Department of Biomedical Engineering, Boston University, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bing","family":"Xia","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, Boston University, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dmitri","family":"Beglov","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, Boston University, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tanggis","family":"Bohnuud","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, Boston University, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nawsad","family":"Alam","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Hebrew University, Jerusalem, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ora","family":"Schueler-Furman","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Hebrew University, Jerusalem, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dima","family":"Kozakov","sequence":"additional","affiliation":[{"name":"Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA"},{"name":"Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,4,18]]},"reference":[{"key":"2023020207513441800_btx216-B1","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1016\/j.str.2015.03.010","article-title":"AnchorDock: blind and flexible anchor-driven peptide docking","volume":"23","author":"Ben-Shimon","year":"2015","journal-title":"Structure"},{"key":"2023020207513441800_btx216-B2","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2023020207513441800_btx216-B3","doi-asserted-by":"crossref","first-page":"1545","DOI":"10.1002\/jcc.21287","article-title":"CHARMM: The biomolecular simulation program","volume":"30","author":"Brooks","year":"2009","journal-title":"J. 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