{"id":"https://openalex.org/W1964668277","doi":"https://doi.org/10.1021/ci300205p","title":"COSMO<i>sim3D</i>: 3D-Similarity and Alignment Based on COSMO Polarization Charge Densities","display_name":"COSMO<i>sim3D</i>: 3D-Similarity and Alignment Based on COSMO Polarization Charge Densities","publication_year":2012,"publication_date":"2012-07-18","ids":{"openalex":"https://openalex.org/W1964668277","doi":"https://doi.org/10.1021/ci300205p","mag":"1964668277","pmid":"https://pubmed.ncbi.nlm.nih.gov/22804925"},"language":"en","primary_location":{"id":"doi:10.1021/ci300205p","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci300205p","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":true,"oa_status":"green","oa_url":"https://zenodo.org/record/1452363","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103190770","display_name":"Michael Thormann","orcid":"https://orcid.org/0009-0001-3826-5851"},"institutions":[{"id":"https://openalex.org/I122754167","display_name":"Medigene (Germany)","ror":"https://ror.org/03kkjyc12","country_code":"DE","type":"company","lineage":["https://openalex.org/I122754167"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Michael Thormann","raw_affiliation_strings":["Origenis GmbH,\rAm Klopferspitz\r19A, 82152 Martinsried, Germany","Origenis GmbH, Am Klopferspitz 19A, 82152 Martinsried, Germany"],"affiliations":[{"raw_affiliation_string":"Origenis GmbH,\rAm Klopferspitz\r19A, 82152 Martinsried, Germany","institution_ids":["https://openalex.org/I122754167"]},{"raw_affiliation_string":"Origenis GmbH, Am Klopferspitz 19A, 82152 Martinsried, Germany","institution_ids":["https://openalex.org/I122754167"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071201468","display_name":"Andreas Klamt","orcid":"https://orcid.org/0000-0002-5320-6219"},"institutions":[{"id":"https://openalex.org/I60668342","display_name":"University of Regensburg","ror":"https://ror.org/01eezs655","country_code":"DE","type":"education","lineage":["https://openalex.org/I60668342"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Andreas Klamt","raw_affiliation_strings":["COSMOlogic GmbH\rand Co. KG, Burscheider Str. 515, 51381 Leverkusen, Germany","Inst. of Physical and Theor. Chemistry,\rUniversity of Regensburg, 93053 Regensburg, Germany","Inst. of Physical and Theor. Chemistry,#R#University of Regensburg, 93053 Regensburg, Germany"],"affiliations":[{"raw_affiliation_string":"COSMOlogic GmbH\rand Co. KG, Burscheider Str. 515, 51381 Leverkusen, Germany","institution_ids":[]},{"raw_affiliation_string":"Inst. of Physical and Theor. Chemistry,\rUniversity of Regensburg, 93053 Regensburg, Germany","institution_ids":["https://openalex.org/I60668342"]},{"raw_affiliation_string":"Inst. of Physical and Theor. Chemistry,#R#University of Regensburg, 93053 Regensburg, Germany","institution_ids":["https://openalex.org/I60668342"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053752483","display_name":"Karin Wichmann","orcid":"https://orcid.org/0000-0001-5743-1141"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Karin Wichmann","raw_affiliation_strings":["COSMOlogic GmbH\rand Co. KG, Burscheider Str. 515, 51381 Leverkusen, Germany","COSMOlogic GmbH#R#and Co. KG, Burscheider Str. 515, 51381 Leverkusen, Germany"],"affiliations":[{"raw_affiliation_string":"COSMOlogic GmbH\rand Co. KG, Burscheider Str. 515, 51381 Leverkusen, Germany","institution_ids":[]},{"raw_affiliation_string":"COSMOlogic GmbH#R#and Co. KG, Burscheider Str. 515, 51381 Leverkusen, Germany","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5103190770"],"corresponding_institution_ids":["https://openalex.org/I122754167"],"apc_list":null,"apc_paid":null,"fwci":0.301,"has_fulltext":false,"cited_by_count":23,"citation_normalized_percentile":{"value":0.53479177,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"52","issue":"8","first_page":"2149","last_page":"2156"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9872999787330627,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9872999787330627,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12613","display_name":"X-ray Diffraction in Crystallography","score":0.9689000248908997,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11177","display_name":"Spectroscopy and Quantum Chemical Studies","score":0.9659000039100647,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/cosmo-rs","display_name":"COSMO-RS","score":0.6018534302711487},{"id":"https://openalex.org/keywords/polarization","display_name":"Polarization (electrochemistry)","score":0.4834612309932709},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4688037037849426},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.3490036725997925},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3154589533805847},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2605057954788208},{"id":"https://openalex.org/keywords/physical-chemistry","display_name":"Physical chemistry","score":0.18638989329338074},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15647247433662415}],"concepts":[{"id":"https://openalex.org/C2775973084","wikidata":"https://www.wikidata.org/wiki/Q17007937","display_name":"COSMO-RS","level":4,"score":0.6018534302711487},{"id":"https://openalex.org/C205049153","wikidata":"https://www.wikidata.org/wiki/Q2698605","display_name":"Polarization (electrochemistry)","level":2,"score":0.4834612309932709},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4688037037849426},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3490036725997925},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3154589533805847},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2605057954788208},{"id":"https://openalex.org/C147789679","wikidata":"https://www.wikidata.org/wiki/Q11372","display_name":"Physical chemistry","level":1,"score":0.18638989329338074},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15647247433662415},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C161790260","wikidata":"https://www.wikidata.org/wiki/Q82264","display_name":"Catalysis","level":2,"score":0.0},{"id":"https://openalex.org/C154881586","wikidata":"https://www.wikidata.org/wiki/Q898579","display_name":"Ionic liquid","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D007536","descriptor_name":"Isomerism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007536","descriptor_name":"Isomerism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007536","descriptor_name":"Isomerism","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":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062313","descriptor_name":"Databases, Pharmaceutical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062313","descriptor_name":"Databases, Pharmaceutical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062313","descriptor_name":"Databases, Pharmaceutical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/ci300205p","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci300205p","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:22804925","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22804925","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},{"id":"pmh:oai:zenodo.org:1452363","is_oa":true,"landing_page_url":"https://zenodo.org/record/1452363","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"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":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:zenodo.org:1452363","is_oa":true,"landing_page_url":"https://zenodo.org/record/1452363","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"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":"","raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[{"score":0.5099999904632568,"id":"https://metadata.un.org/sdg/16","display_name":"Peace, Justice and strong institutions"},{"score":0.4699999988079071,"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W187734647","https://openalex.org/W1562347366","https://openalex.org/W1971578904","https://openalex.org/W1995507794","https://openalex.org/W1995743463","https://openalex.org/W2032245355","https://openalex.org/W2047814942","https://openalex.org/W2055563809","https://openalex.org/W2059964057","https://openalex.org/W2073328513","https://openalex.org/W2089545684","https://openalex.org/W2125285583","https://openalex.org/W2162235098","https://openalex.org/W2169678694"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W2935759653","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W2062208111","https://openalex.org/W1976181487"],"abstract_inverted_index":{"COSMO":[0],"\u03c3-surfaces":[1],"resulting":[2],"from":[3],"quantum":[4],"chemical":[5],"calculations":[6],"of":[7,34,48,54,56,63,68,93,117,121,128,150,167],"molecules":[8],"in":[9,37,142,144,189],"a":[10,24,45,87,102,164,173,198,205],"simulated":[11],"conductor,":[12],"and":[13,27,89,131,140,156,170,178,200],"their":[14],"histograms,":[15],"the":[16,32,52,61,65,94,115,118,122,129,132,148,160,190],"so-called":[17],"\u03c3-profiles,":[18,57],"are":[19,193],"widely":[20],"proven":[21],"to":[22,110,146],"provide":[23],"very":[25,201],"suitable":[26],"almost":[28],"complete":[29],"basis":[30,53,116],"for":[31,172,204],"description":[33],"molecular":[35,49,69],"interactions":[36],"condensed":[38],"systems.":[39],"The":[40,135],"COSMOsim":[41,95],"method":[42,107,203],"therefore":[43],"introduced":[44],"global":[46],"measure":[47,111],"similarity":[50,55,169],"on":[51,101,114],"but":[58],"it":[59],"had":[60],"disadvantage":[62,79],"neglecting":[64],"3D":[66,119],"distribution":[67],"polarities,":[70],"which":[71,85,97],"is":[72,80,86,108,138,163],"crucially":[73],"determining":[74],"all":[75],"ligand-receptor":[76],"binding.":[77],"This":[78,105,158],"now":[81],"overcome":[82],"by":[83],"COSMOsim3D,":[84],"logical":[88],"physically":[90],"sound":[91],"extension":[92],"method,":[96],"uses":[98],"local":[99,151],"\u03c3-profiles":[100],"spatial":[103],"grid.":[104],"new":[106],"used":[109],"intermolecular":[112],"similarities":[113,153],"representation":[120],"surface":[123],"polarization":[124],"charge":[125],"densities":[126],"\u03c3":[127],"target":[130,155],"probe":[133,136],"molecule.":[134],"molecule":[137],"translated":[139],"rotated":[141],"space":[143],"order":[145],"maximize":[147],"sum":[149],"\u03c3-profile":[152],"between":[154,176],"probe.":[157],"sum,":[159],"COSMOsim3D":[161,196],"similarity,":[162],"powerful":[165],"descriptor":[166],"ligand":[168],"allows":[171],"good":[174],"discrimination":[175],"bioisosters":[177],"random":[179],"pairs.":[180],"Validation":[181],"experiments":[182],"using":[183],"about":[184],"600":[185],"pharmacological":[186],"activity":[187],"classes":[188],"MDDR":[191],"database":[192],"given.":[194],"Furthermore,":[195],"represents":[197],"unique":[199],"robust":[202],"field-based":[206],"ligand-ligand":[207],"alignment.":[208]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":4},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2016-06-24T00:00:00"}