{"id":"https://openalex.org/W4367669413","doi":"https://doi.org/10.1021/acs.jcim.3c00336","title":"Binding Site Detection Remastered: Enabling Fast, Robust, and Reliable Binding Site Detection and Descriptor Calculation with DoGSite3","display_name":"Binding Site Detection Remastered: Enabling Fast, Robust, and Reliable Binding Site Detection and Descriptor Calculation with DoGSite3","publication_year":2023,"publication_date":"2023-05-02","ids":{"openalex":"https://openalex.org/W4367669413","doi":"https://doi.org/10.1021/acs.jcim.3c00336","pmid":"https://pubmed.ncbi.nlm.nih.gov/37130052"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c00336","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00336","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075153136","display_name":"Joel Graef","orcid":"https://orcid.org/0000-0001-8327-4936"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Joel Graef","raw_affiliation_strings":["Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics, Bundesstra\u00dfe 43, 20146 Hamburg, Germany"],"raw_orcid":"https://orcid.org/0000-0001-8327-4936","affiliations":[{"raw_affiliation_string":"Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics, Bundesstra\u00dfe 43, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052764114","display_name":"Christiane Ehrt","orcid":"https://orcid.org/0000-0003-1428-0042"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Christiane Ehrt","raw_affiliation_strings":["Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics, Bundesstra\u00dfe 43, 20146 Hamburg, Germany"],"raw_orcid":"https://orcid.org/0000-0003-1428-0042","affiliations":[{"raw_affiliation_string":"Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics, Bundesstra\u00dfe 43, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083205378","display_name":"Matthias Rarey","orcid":"https://orcid.org/0000-0002-9553-6531"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Matthias Rarey","raw_affiliation_strings":["Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics, Bundesstra\u00dfe 43, 20146 Hamburg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-9553-6531","affiliations":[{"raw_affiliation_string":"Universit\u00e4t Hamburg, ZBH - Center for Bioinformatics, Bundesstra\u00dfe 43, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5083205378"],"corresponding_institution_ids":["https://openalex.org/I159176309"],"apc_list":null,"apc_paid":null,"fwci":21.3124,"has_fulltext":false,"cited_by_count":111,"citation_normalized_percentile":{"value":0.99613385,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"63","issue":"10","first_page":"3128","last_page":"3137"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"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":0.9998000264167786,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9995999932289124,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9976999759674072,"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/computer-science","display_name":"Computer science","score":0.6742000579833984},{"id":"https://openalex.org/keywords/grid","display_name":"Grid","score":0.5391038060188293},{"id":"https://openalex.org/keywords/gaussian","display_name":"Gaussian","score":0.5247243046760559},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4751315414905548},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.4299023747444153},{"id":"https://openalex.org/keywords/filter","display_name":"Filter (signal processing)","score":0.41999825835227966},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.41718176007270813},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.41355302929878235},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.389647901058197},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37756577134132385},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.16967952251434326},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.16581037640571594},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.09036040306091309},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08606094121932983}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6742000579833984},{"id":"https://openalex.org/C187691185","wikidata":"https://www.wikidata.org/wiki/Q2020720","display_name":"Grid","level":2,"score":0.5391038060188293},{"id":"https://openalex.org/C163716315","wikidata":"https://www.wikidata.org/wiki/Q901177","display_name":"Gaussian","level":2,"score":0.5247243046760559},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4751315414905548},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.4299023747444153},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.41999825835227966},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.41718176007270813},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.41355302929878235},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.389647901058197},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37756577134132385},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.16967952251434326},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16581037640571594},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.09036040306091309},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08606094121932983},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","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":"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":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.3c00336","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00336","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:37130052","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37130052","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5799999833106995,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G8578832010","display_name":null,"funder_award_id":"031L0172","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G8942490779","display_name":null,"funder_award_id":"031L0105","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W1969017960","https://openalex.org/W1969178306","https://openalex.org/W1970799005","https://openalex.org/W1979914800","https://openalex.org/W1980969309","https://openalex.org/W1981064967","https://openalex.org/W1993046136","https://openalex.org/W1997172276","https://openalex.org/W2000061529","https://openalex.org/W2005481380","https://openalex.org/W2010099233","https://openalex.org/W2018661561","https://openalex.org/W2019951137","https://openalex.org/W2025458374","https://openalex.org/W2031194866","https://openalex.org/W2058463742","https://openalex.org/W2079953901","https://openalex.org/W2091563009","https://openalex.org/W2103794058","https://openalex.org/W2116993067","https://openalex.org/W2130479394","https://openalex.org/W2132395520","https://openalex.org/W2140538197","https://openalex.org/W2146041471","https://openalex.org/W2149095014","https://openalex.org/W2158714788","https://openalex.org/W2160544139","https://openalex.org/W2164088236","https://openalex.org/W2169434145","https://openalex.org/W2238707319","https://openalex.org/W2265102996","https://openalex.org/W2474188283","https://openalex.org/W2610550630","https://openalex.org/W2611792444","https://openalex.org/W2716141585","https://openalex.org/W2768092025","https://openalex.org/W2800222455","https://openalex.org/W2900167333","https://openalex.org/W2948308941","https://openalex.org/W2950200056","https://openalex.org/W3005776600","https://openalex.org/W3046345744","https://openalex.org/W3088634596","https://openalex.org/W3177828909","https://openalex.org/W3197223249","https://openalex.org/W4229031603","https://openalex.org/W4248107770","https://openalex.org/W6833262612"],"related_works":["https://openalex.org/W2480711475","https://openalex.org/W2061997414","https://openalex.org/W1587522533","https://openalex.org/W2153190755","https://openalex.org/W2121182182","https://openalex.org/W1996411829","https://openalex.org/W3017600601","https://openalex.org/W135095951","https://openalex.org/W2044905153","https://openalex.org/W2561730314"],"abstract_inverted_index":{"Binding":[0],"site":[1,66,85],"prediction":[2],"on":[3,46,63,103],"protein":[4,48],"structures":[5],"is":[6,34],"a":[7,35,40,108],"crucial":[8],"step":[9],"in":[10,60,68],"early":[11],"phase":[12],"drug":[13],"discovery":[14],"whenever":[15],"experimental":[16],"or":[17],"predicted":[18],"structure":[19],"models":[20],"are":[21],"involved.":[22],"DoGSite":[23,102],"belongs":[24],"to":[25,43,97],"the":[26,47,53,69,91],"widely":[27],"used":[28],"tools":[29],"for":[30,76,107],"this":[31,57],"task.":[32],"It":[33],"grid-based":[36],"method":[37],"that":[38],"uses":[39],"Difference-of-Gaussian":[41],"filter":[42],"detect":[44],"cavities":[45],"surface.":[49],"We":[50],"recently":[51],"reimplemented":[52],"first":[54],"version":[55],"of":[56,71],"method,":[58],"released":[59],"2010,":[61],"focusing":[62],"improved":[64],"binding":[65,84],"detection":[67],"presence":[70],"ligands":[72],"and":[73,80,83,100],"optimized":[74],"parameters":[75],"more":[77],"robust,":[78],"reliable,":[79],"fast":[81],"predictions":[82],"descriptor":[86],"calculations.":[87],"Here,":[88],"we":[89],"introduce":[90],"new":[92],"version,":[93],"DoGSite3,":[94],"compare":[95],"it":[96],"its":[98],"predecessor,":[99],"re-evaluate":[101],"published":[104],"data":[105],"sets":[106],"large-scale":[109],"comparative":[110],"performance":[111],"evaluation.":[112]},"counts_by_year":[{"year":2026,"cited_by_count":11},{"year":2025,"cited_by_count":53},{"year":2024,"cited_by_count":36},{"year":2023,"cited_by_count":11}],"updated_date":"2026-05-12T08:28:47.272897","created_date":"2025-10-10T00:00:00"}
