{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,27]],"date-time":"2026-06-27T07:00:02Z","timestamp":1782543602728,"version":"3.54.5"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2020,5,16]],"date-time":"2020-05-16T00:00:00Z","timestamp":1589587200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Spanish Plataforma - Instituto Nacional de Bioinform\u00e1tica","award":["ISCIII-PT17.0009.0022"],"award-info":[{"award-number":["ISCIII-PT17.0009.0022"]}]},{"name":"European project ELIXIR-EXCELERATE","award":["INFRADEV- 1-H2020 Code 676559"],"award-info":[{"award-number":["INFRADEV- 1-H2020 Code 676559"]}]},{"DOI":"10.13039\/100009473","name":"University of Malaga","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009473","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,30]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Molecular docking is aimed at predicting the conformation of small-molecule (ligands) within an identified binding site (BS) in a target protein (receptor). Protein\u2013ligand docking plays an important role in modern drug discovery and biochemistry for protein engineering. However, efficient docking analysis of proteins requires prior knowledge of the BS, which is not always known. The process which covers BS identification and protein\u2013ligand docking usually requires the combination of different programs, which require several input parameters. This is furtherly aggravated when factoring in computational demands, such as CPU-time. Therefore, these types of simulation experiments can become a complex process for researchers without a background in computer sciences.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>To overcome these problems, we have designed an automatic computational workflow (WF) to process protein\u2013ligand complexes, which runs from the identification of the possible BSs positions to the prediction of the experimental binding modes and affinities of the ligand. This open-access WF runs under the Galaxy platform that integrates public domain software. The results of the proposed method are in close agreement with state-of-the-art docking software.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>Software is available at: https:\/\/pistacho.ac.uma.es\/galaxy-bitlab.<\/jats:p><\/jats:sec><jats:sec><jats:title>Contact<\/jats:title><jats:p>euv@uma.es<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa481","type":"journal-article","created":{"date-parts":[[2020,5,12]],"date-time":"2020-05-12T03:19:29Z","timestamp":1589253569000},"page":"4203-4205","source":"Crossref","is-referenced-by-count":4,"title":["PLIDflow: an open-source workflow for the online analysis of protein\u2013ligand docking using galaxy"],"prefix":"10.1093","volume":"36","author":[{"given":"Eugenia","family":"Ulzurrun","sequence":"first","affiliation":[{"name":"Department of Computer Architecture , Instituto de Investigaci\u00f3n Biom\u00e9dica de M\u00e1laga-IBIMA, University of M\u00e1laga, M\u00e1laga, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yorley","family":"Duarte","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Integrative Biology , Facultad de Ciencias de la Vida, Universidad Andr\u00e9s Bello, Santiago, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Esteban","family":"Perez-Wohlfeil","sequence":"additional","affiliation":[{"name":"Department of Computer Architecture , Instituto de Investigaci\u00f3n Biom\u00e9dica de M\u00e1laga-IBIMA, University of M\u00e1laga, M\u00e1laga, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fernando","family":"Gonzalez-Nilo","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Integrative Biology , Facultad de Ciencias de la Vida, Universidad Andr\u00e9s Bello, Santiago, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oswaldo","family":"Trelles","sequence":"additional","affiliation":[{"name":"Department of Computer Architecture , Instituto de Investigaci\u00f3n Biom\u00e9dica de M\u00e1laga-IBIMA, University of M\u00e1laga, M\u00e1laga, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,5,16]]},"reference":[{"key":"2023062213541744500_btaa481-B1","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s12859-018-2492-8","article-title":"GCAC: galaxy workflow system for predictive model building for virtual screening","volume":"19","author":"Bharti","year":"2019","journal-title":"BMC Bioinformatics"},{"key":"2023062213541744500_btaa481-B2","doi-asserted-by":"crossref","first-page":"e0134273","DOI":"10.1371\/journal.pone.0134273","article-title":"JMS: an open source workflow management system and web-based cluster front-end for high performance computing","volume":"10","author":"Brown","year":"2015","journal-title":"PLoS One"},{"key":"2023062213541744500_btaa481-B3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v061.i06","article-title":"NbClust: an R package for determining the relevant number of clusters in a data set","volume":"61","author":"Charrad","year":"2014","journal-title":"J. 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