{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T10:14:59Z","timestamp":1779185699615,"version":"3.51.4"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2021,5,5]],"date-time":"2021-05-05T00:00:00Z","timestamp":1620172800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002957","name":"Technische Universit\u00e4t Dresden","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002957","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>With the growth of protein structure data, the analysis of molecular interactions between ligands and their target molecules is gaining importance. PLIP, the protein\u2013ligand interaction profiler, detects and visualises these interactions and provides data in formats suitable for further processing. PLIP has proven very successful in applications ranging from the characterisation of docking experiments to the assessment of novel ligand\u2013protein complexes. Besides ligand\u2013protein interactions, interactions with DNA and RNA play a vital role in many applications, such as drugs targeting DNA or RNA-binding proteins. To date, over 7% of all 3D structures in the Protein Data Bank include DNA or RNA. Therefore, we extended PLIP to encompass these important molecules. We demonstrate the power of this extension with examples of a cancer drug binding to a DNA target, and an RNA\u2013protein complex central to a neurological disease. PLIP is available online at https:\/\/plip-tool.biotec.tu-dresden.de and as open source code. So far, the engine has served over a million queries and the source code has been downloaded several thousand times.<\/jats:p>","DOI":"10.1093\/nar\/gkab294","type":"journal-article","created":{"date-parts":[[2021,4,14]],"date-time":"2021-04-14T00:13:27Z","timestamp":1618359207000},"page":"W530-W534","source":"Crossref","is-referenced-by-count":1830,"title":["PLIP 2021: expanding the scope of the protein\u2013ligand interaction profiler to DNA and RNA"],"prefix":"10.1093","volume":"49","author":[{"given":"Melissa F","family":"Adasme","sequence":"first","affiliation":[{"name":"Biotechnology Center (BIOTEC), CMCB, Technische Universit\u00e4t Dresden, Tatzberg 47-49, 01307 Dresden, Germany"}]},{"given":"Katja L","family":"Linnemann","sequence":"additional","affiliation":[{"name":"Biotechnology Center (BIOTEC), CMCB, Technische Universit\u00e4t Dresden, Tatzberg 47-49, 01307 Dresden, Germany"}]},{"given":"Sarah Naomi","family":"Bolz","sequence":"additional","affiliation":[{"name":"Biotechnology Center (BIOTEC), CMCB, Technische Universit\u00e4t Dresden, Tatzberg 47-49, 01307 Dresden, Germany"}]},{"given":"Florian","family":"Kaiser","sequence":"additional","affiliation":[{"name":"PharmAI GmbH, 01307 Dresden, Germany"}]},{"given":"Sebastian","family":"Salentin","sequence":"additional","affiliation":[{"name":"Biotechnology Center (BIOTEC), CMCB, Technische Universit\u00e4t Dresden, Tatzberg 47-49, 01307 Dresden, Germany"}]},{"given":"V\u00a0Joachim","family":"Haupt","sequence":"additional","affiliation":[{"name":"PharmAI GmbH, 01307 Dresden, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2848-6949","authenticated-orcid":false,"given":"Michael","family":"Schroeder","sequence":"additional","affiliation":[{"name":"Biotechnology Center (BIOTEC), CMCB, Technische Universit\u00e4t Dresden, Tatzberg 47-49, 01307 Dresden, Germany"}]}],"member":"286","published-online":{"date-parts":[[2021,5,5]]},"reference":[{"key":"2021070812045814000_B1","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2021070812045814000_B2","doi-asserted-by":"crossref","first-page":"W443","DOI":"10.1093\/nar\/gkv315","article-title":"PLIP: fully automated protein\u2013ligand interaction profiler","volume":"43","author":"Salentin","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2021070812045814000_B3","doi-asserted-by":"crossref","first-page":"117477","DOI":"10.1016\/j.lfs.2020.117477","article-title":"Anti-HCV, nucleotide inhibitors, repurposing against COVID-19","volume":"248","author":"Elfiky","year":"2020","journal-title":"Life Sci."},{"key":"2021070812045814000_B4","doi-asserted-by":"crossref","first-page":"3351","DOI":"10.3390\/molecules23123351","article-title":"Inverse molecular docking as a novel approach to study anticarcinogenic and anti-neuroinflammatory effects of curcumin","volume":"23","author":"Furlan","year":"2018","journal-title":"Molecules"},{"key":"2021070812045814000_B5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.sbi.2016.10.009","article-title":"Antibody recognition of aberrant glycosylation on the surface of cancer cells","volume":"44","author":"Soliman","year":"2017","journal-title":"Curr. 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