{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T13:14:21Z","timestamp":1776431661545,"version":"3.51.2"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2019,3,13]],"date-time":"2019-03-13T00:00:00Z","timestamp":1552435200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004281","name":"National Science Centre","doi-asserted-by":"publisher","award":["MAESTRO2014\/14\/A\/ST6\/00088"],"award-info":[{"award-number":["MAESTRO2014\/14\/A\/ST6\/00088"]}],"id":[{"id":"10.13039\/501100004281","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>CABS-dock standalone is a multiplatform Python package for protein\u2013peptide docking with backbone flexibility. The main feature of the CABS-dock method is its ability to simulate significant backbone flexibility of the entire protein\u2013peptide system in a reasonable computational time. In the default mode, the package runs a simulation of fully flexible peptide searching for a binding site on the surface of a flexible protein receptor. The flexibility level of the molecules may be defined by the user. Furthermore, the CABS-dock standalone application provides users with full control over the docking simulation from the initial setup to the analysis of results. The standalone version is an upgrade of the original web server implementation\u2014it introduces a number of customizable options, provides support for large-sized systems and offers a framework for deeper analysis of docking results.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>CABS-dock standalone is distributed under the MIT licence, which is free for academic and non-profit users. It is implemented in Python and Fortran. The CABS-dock standalone source code, wiki with documentation and examples of use and installation instructions for Linux, macOS and Windows are available in the CABS-dock standalone repository at https:\/\/bitbucket.org\/lcbio\/cabsdock.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz185","type":"journal-article","created":{"date-parts":[[2019,3,12]],"date-time":"2019-03-12T20:13:28Z","timestamp":1552421608000},"page":"4170-4172","source":"Crossref","is-referenced-by-count":84,"title":["CABS-dock standalone: a toolbox for flexible protein\u2013peptide docking"],"prefix":"10.1093","volume":"35","author":[{"given":"Mateusz","family":"Kurcinski","sequence":"first","affiliation":[{"name":"Biological and Chemical Research Centre , Faculty of Chemistry, University of Warsaw, Warsaw, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maciej","family":"Pawel Ciemny","sequence":"additional","affiliation":[{"name":"Biological and Chemical Research Centre , Faculty of Chemistry, University of Warsaw, Warsaw, Poland"},{"name":"University of Warsaw Faculty of Physics, , Warsaw, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tymoteusz","family":"Oleniecki","sequence":"additional","affiliation":[{"name":"Biological and Chemical Research Centre , Faculty of Chemistry, University of Warsaw, Warsaw, Poland"},{"name":"College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw , Warsaw, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aleksander","family":"Kuriata","sequence":"additional","affiliation":[{"name":"Biological and Chemical Research Centre , Faculty of Chemistry, University of Warsaw, Warsaw, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1832-4364","authenticated-orcid":false,"given":"Aleksandra E","family":"Badaczewska-Dawid","sequence":"additional","affiliation":[{"name":"Biological and Chemical Research Centre , Faculty of Chemistry, University of Warsaw, Warsaw, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrzej","family":"Kolinski","sequence":"additional","affiliation":[{"name":"Biological and Chemical Research Centre , Faculty of Chemistry, University of Warsaw, Warsaw, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7623-0935","authenticated-orcid":false,"given":"Sebastian","family":"Kmiecik","sequence":"additional","affiliation":[{"name":"Biological and Chemical Research Centre , Faculty of Chemistry, University of Warsaw, Warsaw, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,3,13]]},"reference":[{"key":"2023013108272732800_btz185-B1","first-page":"bby080","article-title":"Protein\u2013peptide docking using CABS-dock and contact information","author":"Blaszczyk","year":"2018","journal-title":"Brief. 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