{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:44:19Z","timestamp":1753875859287,"version":"3.41.2"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2023,7,20]],"date-time":"2023-07-20T00:00:00Z","timestamp":1689811200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Czech Ministry of Education"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>Access pathways in enzymes are crucial for the passage of substrates and products of catalysed reactions. The process can be studied by computational means with variable degrees of precision. Our in-house approximative method CaverDock provides a fast and easy way to set up and run ligand binding and unbinding calculations through protein tunnels and channels. Here we introduce pyCaverDock, a Python3 API designed to improve user experience with the tool and further facilitate the ligand transport analyses. The API enables users to simplify the steps needed to use CaverDock, from automatizing setup processes to designing screening pipelines.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>pyCaverDock API is implemented in Python 3 and is freely available with detailed documentation and practical examples at https:\/\/loschmidt.chemi.muni.cz\/caverdock\/.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad443","type":"journal-article","created":{"date-parts":[[2023,7,20]],"date-time":"2023-07-20T19:05:08Z","timestamp":1689879908000},"source":"Crossref","is-referenced-by-count":0,"title":["pyCaverDock: Python implementation of the popular tool for analysis of ligand transport with advanced caching and batch calculation support"],"prefix":"10.1093","volume":"39","author":[{"given":"Ondrej","family":"Vavra","sequence":"first","affiliation":[{"name":"Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University , 625 00 Brno, Czech Republic"},{"name":"International Clinical Research Center, St. Anne\u2019s University Hospital Brno , 656 91 Brno, Czech Republic"}]},{"given":"Jakub","family":"Beranek","sequence":"additional","affiliation":[{"name":"IT4Innovations, VSB \u2013 Technical University of Ostrava , 17. listopadu 2172\/15, 708 00 Ostrava-Poruba, Czech Republic"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3139-3700","authenticated-orcid":false,"given":"Jan","family":"Stourac","sequence":"additional","affiliation":[{"name":"Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University , 625 00 Brno, Czech Republic"},{"name":"International Clinical Research Center, St. Anne\u2019s University Hospital Brno , 656 91 Brno, Czech Republic"}]},{"given":"Martin","family":"Surkovsky","sequence":"additional","affiliation":[{"name":"IT4Innovations, VSB \u2013 Technical University of Ostrava , 17. listopadu 2172\/15, 708 00 Ostrava-Poruba, Czech Republic"}]},{"given":"Jiri","family":"Filipovic","sequence":"additional","affiliation":[{"name":"Institute of Computer Science, Masaryk University , 602 00 Brno, Czech Republic"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7848-8216","authenticated-orcid":false,"given":"Jiri","family":"Damborsky","sequence":"additional","affiliation":[{"name":"Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University , 625 00 Brno, Czech Republic"},{"name":"International Clinical Research Center, St. Anne\u2019s University Hospital Brno , 656 91 Brno, Czech Republic"}]},{"given":"Jan","family":"Martinovic","sequence":"additional","affiliation":[{"name":"IT4Innovations, VSB \u2013 Technical University of Ostrava , 17. listopadu 2172\/15, 708 00 Ostrava-Poruba, Czech Republic"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6803-0340","authenticated-orcid":false,"given":"David","family":"Bednar","sequence":"additional","affiliation":[{"name":"Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University , 625 00 Brno, Czech Republic"},{"name":"International Clinical Research Center, St. Anne\u2019s University Hospital Brno , 656 91 Brno, Czech Republic"}]}],"member":"286","published-online":{"date-parts":[[2023,7,20]]},"reference":[{"key":"2023080305050928800_btad443-B1","doi-asserted-by":"crossref","first-page":"7597","DOI":"10.1021\/acscatal.6b02081","article-title":"Engineering a de novo transport tunnel","volume":"6","author":"Brezovsky","year":"2016","journal-title":"ACS Catal"},{"key":"2023080305050928800_btad443-B2","doi-asserted-by":"crossref","first-page":"e1002708","DOI":"10.1371\/journal.pcbi.1002708","article-title":"CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein 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