{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,6]],"date-time":"2026-04-06T12:26:26Z","timestamp":1775478386851,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2019,8,16]],"date-time":"2019-08-16T00:00:00Z","timestamp":1565913600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union Horizon 2020","award":["675728"],"award-info":[{"award-number":["675728"]}]},{"name":"European Union Horizon 2020","award":["823830"],"award-info":[{"award-number":["823830"]}]},{"name":"EOSC-hub","award":["777536"],"award-info":[{"award-number":["777536"]}]},{"name":"Dutch Foundation for Scientific Research","award":["718.015.001"],"award-info":[{"award-number":["718.015.001"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The use of experimental information has been demonstrated to increase the success rate of computational macromolecular docking. Many methods use information to post-filter the simulation output while others drive the simulation based on experimental restraints, which can become problematic for more complex scenarios such as multiple binding interfaces.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present a novel method for including interface information into protein docking simulations within the LightDock framework. Prior to the simulation, irrelevant regions from the receptor are excluded for sampling (filter of initial swarms) and initial ligand poses are pre-oriented based on ligand input information. We demonstrate the applicability of this approach on the new 55 cases of the Protein\u2013Protein Docking Benchmark 5, using different amounts of information. Even with incomplete or incorrect information, a significant improvement in performance is obtained compared to blind ab initio docking.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The software is supported and freely available from https:\/\/github.com\/brianjimenez\/lightdock and analysis data from https:\/\/github.com\/brianjimenez\/lightdock_bm5.<\/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\/btz642","type":"journal-article","created":{"date-parts":[[2019,8,15]],"date-time":"2019-08-15T15:12:48Z","timestamp":1565881968000},"page":"950-952","source":"Crossref","is-referenced-by-count":43,"title":["LightDock goes information-driven"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6588-624X","authenticated-orcid":false,"given":"Jorge","family":"Roel-Touris","sequence":"first","affiliation":[{"name":"Bijvoet Center for Biomolecular Research, Faculty of Science, Department of Chemistry , Utrecht University, Utrecht, The Netherlands"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7369-1322","authenticated-orcid":false,"given":"Alexandre M J J","family":"Bonvin","sequence":"additional","affiliation":[{"name":"Bijvoet Center for Biomolecular Research, Faculty of Science, Department of Chemistry , Utrecht University, Utrecht, The Netherlands"}]},{"given":"Brian","family":"Jim\u00e9nez-Garc\u00eda","sequence":"additional","affiliation":[{"name":"Bijvoet Center for Biomolecular Research, Faculty of Science, Department of Chemistry , Utrecht University, Utrecht, The Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2019,8,16]]},"reference":[{"key":"2023013110094778100_btz642-B1","doi-asserted-by":"crossref","first-page":"1731","DOI":"10.1021\/ja026939x","article-title":"HADDOCK: a protein\u2013protein docking approach based on biochemical or biophysical information","volume":"125","author":"Dominguez","year":"2003","journal-title":"J. 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