{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T02:14:55Z","timestamp":1774577695042,"version":"3.50.1"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2018,9,20]],"date-time":"2018-09-20T00:00:00Z","timestamp":1537401600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title\/>\n                  <jats:p>CABS-dock is a computational method for protein\u2013peptide molecular docking that does not require predefinition of the binding site. The peptide is treated as fully flexible, while the protein backbone undergoes small fluctuations and, optionally, large-scale rearrangements. Here, we present a specific CABS-dock protocol that enhances the docking procedure using fragmentary information about protein\u2013peptide contacts. The contact information is used to narrow down the search for the binding peptide pose to the proximity of the binding site. We used information on a single-chosen and randomly chosen native protein\u2013peptide contact to validate the protocol on the peptiDB benchmark. The contact information significantly improved CABS-dock performance. The protocol has been made available as a new feature of the CABS-dock web server (at http:\/\/biocomp.chem.uw.edu.pl\/CABSdock\/).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Short abstract<\/jats:title>\n                  <jats:p>CABS-dock is a tool for flexible docking of peptides to proteins. In this article, we present a protocol for CABS-dock docking driven by information about protein\u2013peptide contact(s). Using information on individual protein\u2013peptide contacts allows to improve the accuracy of CABS-dock docking.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bib\/bby080","type":"journal-article","created":{"date-parts":[[2018,9,17]],"date-time":"2018-09-17T23:45:23Z","timestamp":1537227923000},"page":"2299-2305","source":"Crossref","is-referenced-by-count":43,"title":["Protein\u2013peptide docking using CABS-dock and contact information"],"prefix":"10.1093","volume":"20","author":[{"given":"Maciej","family":"Blaszczyk","sequence":"first","affiliation":[{"name":"Biological and Chemical Research Centre, University of Warsaw"}]},{"given":"Maciej Pawel","family":"Ciemny","sequence":"additional","affiliation":[{"name":"Faculty of Physics at the University of Warsaw"}]},{"given":"Andrzej","family":"Kolinski","sequence":"additional","affiliation":[{"name":"University of Warsaw"}]},{"given":"Mateusz","family":"Kurcinski","sequence":"additional","affiliation":[{"name":"Biological 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