{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T15:00:21Z","timestamp":1776092421150,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2022,10,25]],"date-time":"2022-10-25T00:00:00Z","timestamp":1666656000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Grant Agency of Charles University","award":["1038120"],"award-info":[{"award-number":["1038120"]}]},{"name":"ELIXIR CZ Research Infrastructure","award":["LM2018131"],"award-info":[{"award-number":["LM2018131"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,12,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Understanding the mechanism of action of a protein or designing better ligands for it, often requires access to a bound (holo) and an unbound (apo) state of the protein. Resources for the quick and easy retrieval of such conformations are severely limited. Apo\u2013Holo Juxtaposition (AHoJ), is a web application for retrieving apo\u2013holo structure pairs for user-defined ligands. Given a query structure and one or more user-specified ligands, it retrieves all other structures of the same protein that feature the same binding site(s), aligns them, and examines the superimposed binding sites to determine whether each structure is apo or holo, in reference to the query. The resulting superimposed datasets of apo\u2013holo pairs can be visualized and downloaded for further analysis. AHoJ accepts multiple input queries, allowing the creation of customized apo\u2013holo datasets.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Freely available for non-commercial use at http:\/\/apoholo.cz. Source code available at https:\/\/github.com\/cusbg\/AHoJ-project.<\/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\/btac701","type":"journal-article","created":{"date-parts":[[2022,10,25]],"date-time":"2022-10-25T13:54:03Z","timestamp":1666706043000},"page":"5452-5453","source":"Crossref","is-referenced-by-count":11,"title":["AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands"],"prefix":"10.1093","volume":"38","author":[{"given":"Christos P","family":"Feidakis","sequence":"first","affiliation":[{"name":"Department of Cell Biology, Faculty of Science, Charles University , Prague 12843, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Radoslav","family":"Krivak","sequence":"additional","affiliation":[{"name":"Department of Software Engineering, Faculty of Mathematics and Physics, Charles University , Prague 12116, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Hoksza","sequence":"additional","affiliation":[{"name":"Department of Software Engineering, Faculty of Mathematics and Physics, Charles University , Prague 12116, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8788-3202","authenticated-orcid":false,"given":"Marian","family":"Novotny","sequence":"additional","affiliation":[{"name":"Department of Cell Biology, Faculty of Science, Charles University , Prague 12843, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,10,25]]},"reference":[{"key":"2023030411460622700_","doi-asserted-by":"crossref","first-page":"2271","DOI":"10.1016\/j.bpj.2018.02.038","article-title":"Ensemble docking in drug discovery","volume":"114","author":"Amaro","year":"2018","journal-title":"Biophys. 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