{"id":"https://openalex.org/W4223432929","doi":"https://doi.org/10.1093/nar/gkac250","title":"3DLigandSite: structure-based prediction of protein\u2013ligand binding sites","display_name":"3DLigandSite: structure-based prediction of protein\u2013ligand binding sites","publication_year":2022,"publication_date":"2022-04-12","ids":{"openalex":"https://openalex.org/W4223432929","doi":"https://doi.org/10.1093/nar/gkac250","pmid":"https://pubmed.ncbi.nlm.nih.gov/35412635"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkac250","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkac250","pdf_url":"https://academic.oup.com/nar/article-pdf/50/W1/W13/44377423/gkac250.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/50/W1/W13/44377423/gkac250.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024306165","display_name":"Jake E McGreig","orcid":"https://orcid.org/0000-0002-3068-5624"},"institutions":[{"id":"https://openalex.org/I20581793","display_name":"University of Kent","ror":"https://ror.org/00xkeyj56","country_code":"GB","type":"education","lineage":["https://openalex.org/I20581793"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jake E McGreig","raw_affiliation_strings":["School of Biosciences, Division of Natural Sciences, University of Kent , Canterbury , Kent \u00a0CT2 7NJ, UK"],"affiliations":[{"raw_affiliation_string":"School of Biosciences, Division of Natural Sciences, University of Kent , Canterbury , Kent \u00a0CT2 7NJ, UK","institution_ids":["https://openalex.org/I20581793"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052012342","display_name":"Hannah Uri","orcid":null},"institutions":[{"id":"https://openalex.org/I20581793","display_name":"University of Kent","ror":"https://ror.org/00xkeyj56","country_code":"GB","type":"education","lineage":["https://openalex.org/I20581793"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Hannah Uri","raw_affiliation_strings":["School of Biosciences, Division of Natural Sciences, University of Kent , Canterbury , Kent \u00a0CT2 7NJ, UK"],"affiliations":[{"raw_affiliation_string":"School of Biosciences, Division of Natural Sciences, University of Kent , Canterbury , Kent \u00a0CT2 7NJ, UK","institution_ids":["https://openalex.org/I20581793"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009686200","display_name":"Magdalena Antczak","orcid":"https://orcid.org/0000-0003-1503-1849"},"institutions":[{"id":"https://openalex.org/I20581793","display_name":"University of Kent","ror":"https://ror.org/00xkeyj56","country_code":"GB","type":"education","lineage":["https://openalex.org/I20581793"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Magdalena Antczak","raw_affiliation_strings":["School of Biosciences, Division of Natural Sciences, University of Kent , Canterbury , Kent \u00a0CT2 7NJ, UK"],"affiliations":[{"raw_affiliation_string":"School of Biosciences, Division of Natural Sciences, University of Kent , Canterbury , Kent \u00a0CT2 7NJ, UK","institution_ids":["https://openalex.org/I20581793"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023619547","display_name":"Michael J.E. Sternberg","orcid":"https://orcid.org/0000-0002-1884-5445"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Michael J E Sternberg","raw_affiliation_strings":["Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London , London \u00a0SW7 2AZ, UK"],"affiliations":[{"raw_affiliation_string":"Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London , London \u00a0SW7 2AZ, UK","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074740364","display_name":"Martin Michaelis","orcid":"https://orcid.org/0000-0002-5710-5888"},"institutions":[{"id":"https://openalex.org/I20581793","display_name":"University of Kent","ror":"https://ror.org/00xkeyj56","country_code":"GB","type":"education","lineage":["https://openalex.org/I20581793"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Martin Michaelis","raw_affiliation_strings":["School of Biosciences, Division of Natural Sciences, University of Kent , Canterbury , Kent \u00a0CT2 7NJ, UK"],"affiliations":[{"raw_affiliation_string":"School of Biosciences, Division of Natural Sciences, University of Kent , Canterbury , Kent \u00a0CT2 7NJ, UK","institution_ids":["https://openalex.org/I20581793"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054810742","display_name":"Mark N. Wass","orcid":"https://orcid.org/0000-0001-5428-6479"},"institutions":[{"id":"https://openalex.org/I20581793","display_name":"University of Kent","ror":"https://ror.org/00xkeyj56","country_code":"GB","type":"education","lineage":["https://openalex.org/I20581793"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Mark\u00a0N Wass","raw_affiliation_strings":["School of Biosciences, Division of Natural Sciences, University of Kent , Canterbury , Kent \u00a0CT2 7NJ, UK"],"affiliations":[{"raw_affiliation_string":"School of Biosciences, Division of Natural Sciences, University of Kent , Canterbury , Kent \u00a0CT2 7NJ, UK","institution_ids":["https://openalex.org/I20581793"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5054810742"],"corresponding_institution_ids":["https://openalex.org/I20581793"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":7.3681,"has_fulltext":true,"cited_by_count":50,"citation_normalized_percentile":{"value":0.97754124,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"50","issue":"W1","first_page":"W13","last_page":"W20"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9983999729156494,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.6226202249526978},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5904574990272522},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5737952589988708},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4573513865470886},{"id":"https://openalex.org/keywords/web-site","display_name":"Web site","score":0.44845032691955566},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.4426461458206177},{"id":"https://openalex.org/keywords/template","display_name":"Template","score":0.41839799284935},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3743863105773926},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.292609304189682},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2132280468940735},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.1684936285018921},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.14770936965942383}],"concepts":[{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.6226202249526978},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5904574990272522},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5737952589988708},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4573513865470886},{"id":"https://openalex.org/C2984519610","wikidata":"https://www.wikidata.org/wiki/Q35127","display_name":"Web site","level":3,"score":0.44845032691955566},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.4426461458206177},{"id":"https://openalex.org/C82714645","wikidata":"https://www.wikidata.org/wiki/Q438331","display_name":"Template","level":2,"score":0.41839799284935},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3743863105773926},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.292609304189682},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2132280468940735},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.1684936285018921},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.14770936965942383},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gkac250","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkac250","pdf_url":"https://academic.oup.com/nar/article-pdf/50/W1/W13/44377423/gkac250.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:35412635","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35412635","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:kar.kent.ac.uk:93989","is_oa":false,"landing_page_url":"https://doi.org/10.1093/nar%2Fgkac250>)","pdf_url":null,"source":{"id":"https://openalex.org/S4377196264","display_name":"Kent Academic Repository (University of Kent)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20581793","host_organization_name":"University of Kent","host_organization_lineage":["https://openalex.org/I20581793"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"PeerReviewed"},{"id":"pmh:oai:pubmedcentral.nih.gov:9252821","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9252821","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"},{"id":"pmh:oai:spiral.imperial.ac.uk:10044/1/96374","is_oa":true,"landing_page_url":"http://hdl.handle.net/10044/1/96374","pdf_url":null,"source":{"id":"https://openalex.org/S4306401396","display_name":"Spiral (Imperial College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I47508984","host_organization_name":"Imperial College London","host_organization_lineage":["https://openalex.org/I47508984"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"W1=20","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/nar/gkac250","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkac250","pdf_url":"https://academic.oup.com/nar/article-pdf/50/W1/W13/44377423/gkac250.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1934935867","display_name":null,"funder_award_id":"Engineering and Physical Sciences R","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G3952739599","display_name":null,"funder_award_id":"BB/J0105451/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G4597177185","display_name":null,"funder_award_id":"Wellcome Trust","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G6188371866","display_name":null,"funder_award_id":"218242/Z/19/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G6758540359","display_name":null,"funder_award_id":"WT104955MA","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G7286887268","display_name":null,"funder_award_id":"BB/J019240/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4223432929.pdf","grobid_xml":"https://content.openalex.org/works/W4223432929.grobid-xml"},"referenced_works_count":66,"referenced_works":["https://openalex.org/W1545127980","https://openalex.org/W1803102843","https://openalex.org/W1927265873","https://openalex.org/W1967293793","https://openalex.org/W1976526581","https://openalex.org/W2000588380","https://openalex.org/W2003656858","https://openalex.org/W2018397599","https://openalex.org/W2032426558","https://openalex.org/W2051210555","https://openalex.org/W2081491073","https://openalex.org/W2083589318","https://openalex.org/W2090649877","https://openalex.org/W2102245393","https://openalex.org/W2104601544","https://openalex.org/W2108516632","https://openalex.org/W2109553965","https://openalex.org/W2110800533","https://openalex.org/W2126016150","https://openalex.org/W2131617076","https://openalex.org/W2132395520","https://openalex.org/W2140735973","https://openalex.org/W2143286837","https://openalex.org/W2144258433","https://openalex.org/W2145268834","https://openalex.org/W2146233784","https://openalex.org/W2158964183","https://openalex.org/W2160085559","https://openalex.org/W2170747616","https://openalex.org/W2178411042","https://openalex.org/W2227395312","https://openalex.org/W2530905855","https://openalex.org/W2550969987","https://openalex.org/W2557595285","https://openalex.org/W2576831217","https://openalex.org/W2617750324","https://openalex.org/W2738813620","https://openalex.org/W2765284721","https://openalex.org/W2807540482","https://openalex.org/W2883966645","https://openalex.org/W2887981960","https://openalex.org/W2911404893","https://openalex.org/W2916930667","https://openalex.org/W2950200056","https://openalex.org/W2950954328","https://openalex.org/W2957309664","https://openalex.org/W2972411752","https://openalex.org/W2978232173","https://openalex.org/W2982977147","https://openalex.org/W2989608901","https://openalex.org/W3005669732","https://openalex.org/W3007743886","https://openalex.org/W3012511738","https://openalex.org/W3035958189","https://openalex.org/W3112376646","https://openalex.org/W3116801402","https://openalex.org/W3126222000","https://openalex.org/W3165603781","https://openalex.org/W3177828909","https://openalex.org/W3197066654","https://openalex.org/W3197082762","https://openalex.org/W3211795435","https://openalex.org/W3214131546","https://openalex.org/W4239510810","https://openalex.org/W6769535376","https://openalex.org/W6778269158"],"related_works":["https://openalex.org/W2121300814","https://openalex.org/W4234406076","https://openalex.org/W1886613375","https://openalex.org/W4236081792","https://openalex.org/W4250583430","https://openalex.org/W2010731026","https://openalex.org/W2360893094","https://openalex.org/W4390787808","https://openalex.org/W4236036386","https://openalex.org/W2025584407"],"abstract_inverted_index":{"3DLigandSite":[0,24,139,167],"is":[1,168],"a":[2,16,76,106,123,134,141,175],"web":[3],"tool":[4],"for":[5,126,153,163],"the":[6,20,31,51,58,63,96,100,111,117,193,196],"prediction":[7,113],"of":[8,23,119,133,138,143,192],"ligand-binding":[9,97],"sites":[10,36,43,146,156],"in":[11,25,37,44,99,183],"proteins.":[12],"Here,":[13],"we":[14,104],"report":[15],"significant":[17],"update":[18],"since":[19],"first":[21],"release":[22],"2010.":[26],"The":[27],"overall":[28],"methodology":[29],"remains":[30],"same,":[32],"with":[33,88],"candidate":[34],"binding":[35,42,135,145,155,165,198],"proteins":[38],"inferred":[39],"using":[40,79],"known":[41],"related":[45],"protein":[46,176,194],"structures":[47,61,71,87],"as":[48,110],"templates.":[49],"However,":[50],"initial":[52],"structural":[53],"modelling":[54],"step":[55],"now":[56],"uses":[57],"newly":[59],"available":[60,169],"from":[62],"AlphaFold":[64,70],"database":[65],"or":[66,178],"alternatively":[67],"Phyre2":[68],"when":[69],"are":[72,92,181],"not":[73],"available.":[74],"Further,":[75],"sequence-based":[77],"search":[78],"HHSearch":[80],"has":[81],"been":[82],"introduced":[83,105],"to":[84,94,130],"identify":[85],"template":[86],"bound":[89],"ligands":[90],"that":[91],"used":[93],"infer":[95],"residues":[98],"query":[101],"protein.":[102],"Finally,":[103],"machine":[107],"learning":[108],"element":[109],"final":[112],"step,":[114],"which":[115],"improves":[116],"accuracy":[118],"predictions":[120],"and":[121,157,195],"provides":[122],"confidence":[124],"score":[125],"each":[127],"residue":[128],"predicted":[129,197],"be":[131],"part":[132],"site.":[136],"Validation":[137],"on":[140],"set":[142],"6416":[144],"obtained":[147],"92%":[148],"recall":[149,159],"at":[150,160,170],"75%":[151,161],"precision":[152,162],"non-metal":[154],"52%":[158],"metal":[164],"sites.":[166,199],"https://www.wass-michaelislab.org/3dligandsite.":[171],"Users":[172],"submit":[173],"either":[174],"sequence":[177],"structure.":[179],"Results":[180],"displayed":[182],"multiple":[184],"formats":[185],"including":[186],"an":[187],"interactive":[188],"Mol*":[189],"molecular":[190],"visualization":[191]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":15},{"year":2023,"cited_by_count":18},{"year":2022,"cited_by_count":4}],"updated_date":"2026-03-07T16:01:11.037858","created_date":"2025-10-10T00:00:00"}
