{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T14:39:15Z","timestamp":1782398355488,"version":"3.54.5"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2016,11,22]],"date-time":"2016-11-22T00:00:00Z","timestamp":1479772800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"Consejer\u00eda de Educaci\u00f3n"},{"DOI":"10.13039\/501100008530","name":"FEDER","doi-asserted-by":"crossref","award":["SA147U13"],"award-info":[{"award-number":["SA147U13"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100008530","name":"FEDER","doi-asserted-by":"crossref","award":["SA030U16"],"award-info":[{"award-number":["SA030U16"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>AutoDock is a very popular software package for docking and virtual screening. However, currently it is hard work to visualize more than one result from the virtual screening at a time. To overcome this limitation we have designed JADOPPT, a tool for automatically preparing and processing multiple ligand-protein docked poses obtained from AutoDock. It allows the simultaneous visual assessment and comparison of multiple poses through clustering methods. Moreover, it permits the representation of reference ligands with known binding modes, binding site residues, highly scoring regions for the ligand, and the calculated binding energy of the best ranked results.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>JADOPPT, supplementary material (Case Studies 1 and 2) and video tutorials are available at http:\/\/visualanalytics.land\/cgarcia\/JADOPPT.html<\/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\/btw677","type":"journal-article","created":{"date-parts":[[2016,10,25]],"date-time":"2016-10-25T11:05:33Z","timestamp":1477393533000},"page":"583-585","source":"Crossref","is-referenced-by-count":18,"title":["JADOPPT: java based AutoDock preparing and processing tool"],"prefix":"10.1093","volume":"33","author":[{"given":"Carlos","family":"Garc\u00eda-P\u00e9rez","sequence":"first","affiliation":[{"name":"Centro de Biotecnolog\u00eda Gen\u00f3mica, Instituto Polit\u00e9cnico Nacional, Reynosa, Mexico"},{"name":"Departmento de Inform\u00e1tica y Autom\u00e1tica, Salamanca, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rafael","family":"Pel\u00e1ez","sequence":"additional","affiliation":[{"name":"Quimica Farmac\u00e9utica, Salamanca, Spain"},{"name":"Instituto de Investigaci\u00f3n Biom\u00e9dica de Salamanca (IBSAL), Salamanca, Spain"},{"name":"Centro de Investigaci\u00f3n de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Salamanca, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roberto","family":"Ther\u00f3n","sequence":"additional","affiliation":[{"name":"Departmento de Inform\u00e1tica y Autom\u00e1tica, Salamanca, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9","family":"Luis L\u00f3pez-P\u00e9rez","sequence":"additional","affiliation":[{"name":"Quimica Farmac\u00e9utica, Salamanca, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,11,22]]},"reference":[{"key":"2023020204430736800_btw677-B1","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1023\/A:1008100132405","article-title":"Morphological similarity: a 3D molecular similarity method correlated with protein-ligand recognition","volume":"14","author":"Jain","year":"2000","journal-title":"J. Comput. Aided Mol. Des"},{"key":"2023020204430736800_btw677-B7","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1002\/bmb.2006.494034042644","article-title":"Biomolecules in the computer: Jmol to the rescue","volume":"34","author":"Herr\u00e1ez","year":"2006","journal-title":"Biochem. Mol. Biol. Educ."},{"key":"2023020204430736800_btw677-B2","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1007\/s10822-010-9395-8","article-title":"Computer-aided drug design platform using PyMOL","volume":"25","author":"Lill","year":"2011","journal-title":"J. Comput. Aided Mol. Des"},{"key":"2023020204430736800_btw677-B3","doi-asserted-by":"crossref","first-page":"2785","DOI":"10.1002\/jcc.21256","article-title":"AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility","volume":"30","author":"Morris","year":"2009","journal-title":"J. Comput. Chem"},{"key":"2023020204430736800_btw677-B4","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1002\/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B","article-title":"Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function","volume":"19","author":"Morris","year":"1998","journal-title":"J. Comput. Chem"},{"key":"2023020204430736800_btw677-B5","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1007\/s10822-010-9352-6","article-title":"Ligand docking and binding site analysis with PyMOL and Autodock\/Vina","volume":"24","author":"Seeliger","year":"2010","journal-title":"J. Comput. Aided Mol. Des"},{"key":"2023020204430736800_btw677-B6","doi-asserted-by":"crossref","first-page":"1803","DOI":"10.1093\/bioinformatics\/btl197","article-title":"BDT: an easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock","volume":"22","author":"Vaqu\u00e9","year":"2006","journal-title":"Bioinformatics"},{"key":"2023020204430736800_btw677-B8","doi-asserted-by":"crossref","first-page":"126.","DOI":"10.1186\/1471-2105-9-126","article-title":"DOVIS: an implementation for high-throughput virtual screening using AutoDock","volume":"9","author":"Zhang","year":"2008","journal-title":"BMC Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/4\/583\/49037933\/bioinformatics_33_4_583.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/4\/583\/49037933\/bioinformatics_33_4_583.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T04:48:06Z","timestamp":1675313286000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/4\/583\/2736311"}},"subtitle":[],"editor":[{"given":"Anna","family":"Tramontano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2016,11,22]]},"references-count":8,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2017,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw677","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,2,15]]},"published":{"date-parts":[[2016,11,22]]}}}