{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,23]],"date-time":"2026-06-23T10:28:02Z","timestamp":1782210482533,"version":"3.54.5"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2021,4,27]],"date-time":"2021-04-27T00:00:00Z","timestamp":1619481600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01-GM132595"],"award-info":[{"award-number":["R01-GM132595"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100014434","name":"Polish National Agency for Academic Exchange","doi-asserted-by":"publisher","award":["PPN\/BEK\/2018\/1\/00058\/U\/00001"],"award-info":[{"award-number":["PPN\/BEK\/2018\/1\/00058\/U\/00001"]}],"id":[{"id":"10.13039\/501100014434","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004895","name":"European Social Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004895","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>\n               <jats:p>Structure-guided drug design depends on the correct identification of ligands in crystal structures of protein complexes. However, the interpretation of the electron density maps is challenging and often burdened with confirmation bias. Ligand identification can be aided by automatic methods such as CheckMyBlob, a machine learning algorithm that learns to generalize ligand descriptions from sets of moieties deposited in the Protein Data Bank. Here, we present the CheckMyBlob web server, a platform that can identify ligands in unmodeled fragments of electron density maps or validate ligands in existing models. The server processes PDB\/mmCIF and MTZ files and returns a ranking of 10 most likely ligands for each detected electron density blob along with interactive 3D visualizations. Additionally, for each prediction\/validation, a plugin script is generated that enables users to conduct a detailed analysis of the server results in Coot. The CheckMyBlob web server is available at https:\/\/checkmyblob.bioreproducibility.org.<\/jats:p>","DOI":"10.1093\/nar\/gkab296","type":"journal-article","created":{"date-parts":[[2021,4,11]],"date-time":"2021-04-11T11:06:59Z","timestamp":1618139219000},"page":"W86-W92","source":"Crossref","is-referenced-by-count":18,"title":["Recognizing and validating ligands with CheckMyBlob"],"prefix":"10.1093","volume":"49","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9723-525X","authenticated-orcid":false,"given":"Dariusz","family":"Brzezinski","sequence":"first","affiliation":[{"name":"Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA"},{"name":"Institute of Computing Science, Poznan University of Technology, Poznan, 60-965, Poland"},{"name":"Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan,\u00a061-704, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8012-5791","authenticated-orcid":false,"given":"Przemyslaw J","family":"Porebski","sequence":"additional","affiliation":[{"name":"Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6269-3151","authenticated-orcid":false,"given":"Marcin","family":"Kowiel","sequence":"additional","affiliation":[{"name":"Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan,\u00a061-704, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1760-2668","authenticated-orcid":false,"given":"Joanna\u00a0M","family":"Macnar","sequence":"additional","affiliation":[{"name":"Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA"},{"name":"College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw,\u00a002-097, Poland"},{"name":"Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Warsaw, 02-089, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7075-7090","authenticated-orcid":false,"given":"Wladek","family":"Minor","sequence":"additional","affiliation":[{"name":"Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,4,27]]},"reference":[{"key":"2021070812033169300_B1","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1107\/S0907444912044423","article-title":"Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures","volume":"69","author":"Pozharski","year":"2013","journal-title":"Acta Crystallogr. 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Crystallogr."},{"key":"2021070812033169300_B5","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1107\/S0907444912000200","article-title":"Handling ligands with Coot","volume":"68","author":"Debreczeni","year":"2012","journal-title":"Acta Crystallogr. Sect. D Biol. Crystallogr."},{"key":"2021070812033169300_B6","doi-asserted-by":"crossref","first-page":"2230","DOI":"10.1107\/S0907444904012995","article-title":"Modelling bound ligands in protein crystal structures","volume":"60","author":"Zwart","year":"2004","journal-title":"Acta Crystallogr. Sect. D Biol. Crystallogr."},{"key":"2021070812033169300_B7","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1107\/S0907444906023389","article-title":"Assessment of automatic ligand building in ARP \/wARP","volume":"63","author":"Evrard","year":"2007","journal-title":"Acta Crystallogr. Sect. D Biol. 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