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It is shown that SEED allows for consistent computational enrichment of fragment libraries, independent of the effective hit rate. Depending on the actual target protein, true positive rates ranging up to 27% are observed at a cutoff value corresponding to the experimental hit rate. The impact of variations in docking protocols and energy filters is discussed in detail. Remaining issues, limitations, and use cases of SEED are also discussed. Our results show that fragment library selection or enhancement for a particular target is likely to benefit from docking with SEED, suggesting that SEED is a useful resource for fragment screening campaigns. A workflow is presented for the use of the program in virtual screening, including filtering and postprocessing to optimize hit rates.<\/jats:p>","DOI":"10.1021\/acs.jcim.0c00556","type":"journal-article","created":{"date-parts":[[2020,8,21]],"date-time":"2020-08-21T10:07:50Z","timestamp":1598004470000},"page":"4881-4893","source":"Crossref","is-referenced-by-count":20,"title":["Assessment of the Fragment Docking\nProgram SEED"],"prefix":"10.1021","volume":"60","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4127-5724","authenticated-orcid":true,"given":"Kenneth","family":"Goossens","sequence":"first","affiliation":[{"name":"University of Antwerp , , Universiteitsplein 1 , ,","place":["Wilrijk, Belgium, 2610"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9980-1646","authenticated-orcid":true,"given":"Berthold","family":"Wroblowski","sequence":"additional","affiliation":[{"name":"Janssen Research and Development , Turnhoutseweg 30 , ,","place":["Beerse, Belgium, 2340"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3637-7048","authenticated-orcid":true,"given":"Cassiano","family":"Langini","sequence":"additional","affiliation":[{"name":"University of Zurich , , Winterthurerstrasse 190 , ,","place":["Zurich, Switzerland, CH-8057"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1915-3141","authenticated-orcid":true,"given":"Herman","family":"van Vlijmen","sequence":"additional","affiliation":[{"name":"Janssen Research and Development , Turnhoutseweg 30 , ,","place":["Beerse, Belgium, 2340"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2317-6792","authenticated-orcid":true,"given":"Amedeo","family":"Caflisch","sequence":"additional","affiliation":[{"name":"University of Zurich , , Winterthurerstrasse 190 , ,","place":["Zurich, Switzerland, CH-8057"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4450-7677","authenticated-orcid":true,"given":"Hans","family":"De Winter","sequence":"additional","affiliation":[{"name":"University of Antwerp , , Universiteitsplein 1 , ,","place":["Wilrijk, Belgium, 2610"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2020,8,21]]},"reference":[{"key":"2026081804375057600_cit1","doi-asserted-by":"publisher","first-page":"823","DOI":"10.1038\/432823a","article-title":"Chemical space","volume":"432","author":"Kirkpatrick","year":"2004","journal-title":"Nature"},{"key":"2026081804375057600_cit2","doi-asserted-by":"publisher","first-page":"1531","DOI":"10.1126\/science.274.5292.1531","article-title":"Discovering high-affinity\nligands for proteins: SAR by NMR","volume":"274","author":"Shuker","year":"1996","journal-title":"Science"},{"key":"2026081804375057600_cit3","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1016\/j.pbiomolbio.2014.09.007","article-title":"Efficient exploration of chemical\nspace by fragment-based screening","volume":"116","author":"Hall","year":"2014","journal-title":"Prog. 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