{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,11]],"date-time":"2025-12-11T07:34:51Z","timestamp":1765438491122,"version":"3.37.3"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2017,9,18]],"date-time":"2017-09-18T00:00:00Z","timestamp":1505692800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["14-24-00100"],"award-info":[{"award-number":["14-24-00100"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Modelling with multiple servers that use different algorithms for docking results in more reliable predictions of interaction sites. However, the scoring and comparison of all models by an expert is time-consuming and is not feasible for large volumes of data generated by such modelling.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Quality ASsessment of DOcking Models (QASDOM) Server is a simple and efficient tool for real-time simultaneous analysis, scoring and ranking of data sets of receptor\u2013ligand complexes built by a range of docking techniques. This meta-server is designed to analyse large data sets of docking models and rank them by scoring criteria developed in this study. It produces two types of output showing the likelihood of specific residues and clusters of residues to be involved in receptor\u2013ligand interactions and the ranking of models. The server also allows visualizing residues that form interaction sites in the receptor and ligand sequence and displays 3D model structures of the receptor\u2013ligand complexes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability<\/jats:title>\n                  <jats:p>http:\/\/qasdom.eimb.ru.<\/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\/btx591","type":"journal-article","created":{"date-parts":[[2017,9,15]],"date-time":"2017-09-15T19:13:59Z","timestamp":1505502839000},"page":"297-299","source":"Crossref","is-referenced-by-count":11,"title":["Meta-server for automatic analysis, scoring and ranking of docking models"],"prefix":"10.1093","volume":"34","author":[{"given":"Anastasia A","family":"Anashkina","sequence":"first","affiliation":[{"name":"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia"}]},{"given":"Yuri","family":"Kravatsky","sequence":"additional","affiliation":[{"name":"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia"}]},{"given":"Eugene","family":"Kuznetsov","sequence":"additional","affiliation":[{"name":"V. A. Trapeznikov Institute of Control Sciences of Russian Academy of Sciences, Moscow, Russia"}]},{"given":"Alexander A","family":"Makarov","sequence":"additional","affiliation":[{"name":"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5000-1373","authenticated-orcid":false,"given":"Alexei A","family":"Adzhubei","sequence":"additional","affiliation":[{"name":"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia"}]}],"member":"286","published-online":{"date-parts":[[2017,9,18]]},"reference":[{"key":"2023012712233369400_btx591-B1","first-page":"1","article-title":"Left-handed polyproline-II helix revisited: proteins causing proteopathies","author":"Adzhubei","year":"2016","journal-title":"J. Biomol. Struct. Dyn"},{"key":"2023012712233369400_btx591-B2","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1093\/bioinformatics\/btg371","article-title":"ClusPro: an automated docking and discrimination method for the prediction of protein complexes","volume":"20","author":"Comeau","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012712233369400_btx591-B3","doi-asserted-by":"crossref","first-page":"1758","DOI":"10.1161\/ATVBAHA.116.307997","article-title":"Interaction between HIV-1 NEF and Calnexin","volume":"36","author":"Hunegnaw","year":"2016","journal-title":"Arterioscler. Thromb. Vasc. Biol"},{"key":"2023012712233369400_btx591-B4","doi-asserted-by":"crossref","first-page":"2082","DOI":"10.1002\/prot.24428","article-title":"Docking, scoring, and affinity prediction in CAPRI","volume":"81","author":"Lensink","year":"2013","journal-title":"Proteins"},{"key":"2023012712233369400_btx591-B5","doi-asserted-by":"crossref","first-page":"W445","DOI":"10.1093\/nar\/gkq311","article-title":"HexServer: an FFT-based protein docking server powered by graphics processors","volume":"36","author":"Macindoe","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2023012712233369400_btx591-B6","doi-asserted-by":"crossref","first-page":"12045","DOI":"10.3390\/molecules200712045","article-title":"Analysis and ranking of protein-protein docking models using inter-residue contacts and inter-molecular contact maps","volume":"20","author":"Oliva","year":"2015","journal-title":"Molecules"},{"key":"2023012712233369400_btx591-B7","doi-asserted-by":"crossref","DOI":"10.1038\/srep27738","article-title":"Direct interaction of beta-amyloid with Na, K-ATPase as a putative regulator of the enzyme function","volume":"6","author":"Petrushanko","year":"2016","journal-title":"Sci. Rep"},{"key":"2023012712233369400_btx591-B8","doi-asserted-by":"crossref","first-page":"1771","DOI":"10.1093\/bioinformatics\/btu097","article-title":"ZDOCK server: interactive docking prediction of protein\u2013protein complexes and symmetric multimers","volume":"30","author":"Pierce","year":"2014","journal-title":"Bioinformatics"},{"key":"2023012712233369400_btx591-B9","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1093\/bioinformatics\/btt038","article-title":"SwarmDock: a server for flexible protein\u2013protein docking","volume":"29","author":"Torchala","year":"2013","journal-title":"Bioinformatics"},{"key":"2023012712233369400_btx591-B10","doi-asserted-by":"crossref","first-page":"W310","DOI":"10.1093\/nar\/gkl206","article-title":"GRAMM-X public web server for protein\u2013protein docking","volume":"34","author":"Tovchigrechko","year":"2006","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/2\/297\/48913081\/bioinformatics_34_2_297.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/2\/297\/48913081\/bioinformatics_34_2_297.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:07:24Z","timestamp":1674824844000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/2\/297\/4160679"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,9,18]]},"references-count":10,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2018,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx591","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2018,1,15]]},"published":{"date-parts":[[2017,9,18]]}}}