{"id":"https://openalex.org/W2582406409","doi":"https://doi.org/10.1021/acs.jcim.6b00561","title":"Index-Based Searching of Interaction Patterns in Large Collections of Protein\u2013Ligand Interfaces","display_name":"Index-Based Searching of Interaction Patterns in Large Collections of Protein\u2013Ligand Interfaces","publication_year":2017,"publication_date":"2017-01-27","ids":{"openalex":"https://openalex.org/W2582406409","doi":"https://doi.org/10.1021/acs.jcim.6b00561","mag":"2582406409","pmid":"https://pubmed.ncbi.nlm.nih.gov/28128948"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.6b00561","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00561","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/A5052571947","display_name":"Therese Inhester","orcid":null},"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":"Therese Inhester","raw_affiliation_strings":["Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086310415","display_name":"Stefan Bietz","orcid":null},"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":"Stefan Bietz","raw_affiliation_strings":["Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031540817","display_name":"Matthias Hilbig","orcid":null},"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":"Matthias Hilbig","raw_affiliation_strings":["Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084532803","display_name":"Robert Schmidt","orcid":"https://orcid.org/0000-0002-7089-4842"},"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":"Robert Schmidt","raw_affiliation_strings":["Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, University of Hamburg, Bundesstrasse 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":["Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-9553-6531","affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5083205378"],"corresponding_institution_ids":["https://openalex.org/I159176309"],"apc_list":null,"apc_paid":null,"fwci":2.3926,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.89566645,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"57","issue":"2","first_page":"148","last_page":"158"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9975000023841858,"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":0.9975000023841858,"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":0.996399998664856,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9951000213623047,"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":0.7545108795166016},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6670517325401306},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.4887990653514862},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4533502459526062},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4458417296409607},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4404706656932831},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.43751227855682373},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.21335655450820923},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11122384667396545}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7545108795166016},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6670517325401306},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.4887990653514862},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4533502459526062},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4458417296409607},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4404706656932831},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.43751227855682373},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.21335655450820923},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11122384667396545},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.6b00561","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00561","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:28128948","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28128948","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":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.5099999904632568}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W1518170439","https://openalex.org/W1970799005","https://openalex.org/W1970981633","https://openalex.org/W1974158203","https://openalex.org/W1982885147","https://openalex.org/W2000061529","https://openalex.org/W2007570703","https://openalex.org/W2007615306","https://openalex.org/W2013863297","https://openalex.org/W2016155858","https://openalex.org/W2021206196","https://openalex.org/W2036305123","https://openalex.org/W2045284802","https://openalex.org/W2059924427","https://openalex.org/W2063475221","https://openalex.org/W2072287929","https://openalex.org/W2083403082","https://openalex.org/W2090157995","https://openalex.org/W2096725584","https://openalex.org/W2100598991","https://openalex.org/W2120138074","https://openalex.org/W2123321071","https://openalex.org/W2130479394","https://openalex.org/W2143482176","https://openalex.org/W2226713891"],"related_works":["https://openalex.org/W2140798747","https://openalex.org/W2948169060","https://openalex.org/W2730112582","https://openalex.org/W2110696645","https://openalex.org/W2358580169","https://openalex.org/W2111347279","https://openalex.org/W2487211728","https://openalex.org/W2378096925","https://openalex.org/W2485376993","https://openalex.org/W2348031209"],"abstract_inverted_index":{"Comparison":[0],"of":[1,8,51,83,112,123,134],"three-dimensional":[2],"interaction":[3],"patterns":[4,40],"in":[5,23,41,86,91,100,136],"large":[6,87],"collections":[7,90],"protein-ligand":[9,17,42,113],"interfaces":[10],"is":[11,76],"a":[12,70,81,92],"key":[13],"element":[14],"for":[15,38,80],"understanding":[16],"interactions":[18],"and":[19,63],"supports":[20],"various":[21],"steps":[22],"the":[24,52,121,124,132],"structure-based":[25,137],"drug":[26],"design":[27,138],"process.":[28],"Different":[29],"methods":[30],"exist":[31],"that":[32,75,104],"provide":[33],"query":[34,57],"systems":[35],"to":[36,78],"search":[37,61,79],"geometrical":[39,84],"complexes.":[43,114],"However,":[44],"these":[45],"tools":[46],"do":[47],"not":[48],"meet":[49],"all":[50],"requirements,":[53],"which":[54],"are":[55,98],"high":[56,64],"variability,":[58],"an":[59,101],"adjustable":[60],"set,":[62],"retrieval":[65],"speed.":[66],"Here":[67],"we":[68],"present":[69,116],"new":[71],"tool":[72],"named":[73],"PELIKAN":[74,125,135],"able":[77],"variety":[82],"queries":[85,119],"protein":[88],"structure":[89],"reasonably":[93],"short":[94],"time.":[95],"The":[96],"data":[97],"stored":[99],"SQLite":[102],"database":[103],"can":[105],"easily":[106],"be":[107],"constructed":[108],"from":[109],"any":[110],"set":[111],"We":[115],"different":[117],"test":[118],"demonstrating":[120],"performance":[122],"approach.":[126],"Furthermore,":[127],"two":[128],"application":[129],"scenarios":[130],"show":[131],"usefulness":[133],"endeavors.":[139]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":5}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}
