{"id":"https://openalex.org/W2755903007","doi":"https://doi.org/10.1021/acs.jcim.7b00291","title":"<i>NAOMI</i>nova: Interactive Geometric Analysis of Noncovalent Interactions in Macromolecular Structures","display_name":"<i>NAOMI</i>nova: Interactive Geometric Analysis of Noncovalent Interactions in Macromolecular Structures","publication_year":2017,"publication_date":"2017-09-11","ids":{"openalex":"https://openalex.org/W2755903007","doi":"https://doi.org/10.1021/acs.jcim.7b00291","mag":"2755903007","pmid":"https://pubmed.ncbi.nlm.nih.gov/28891648"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.7b00291","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.7b00291","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":true,"raw_author_name":"Therese Inhester","raw_affiliation_strings":["ZBH - Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany"],"affiliations":[{"raw_affiliation_string":"ZBH - Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077542460","display_name":"Eva Nittinger","orcid":"https://orcid.org/0000-0001-7231-7996"},"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":"Eva Nittinger","raw_affiliation_strings":["ZBH - Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany"],"affiliations":[{"raw_affiliation_string":"ZBH - Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019475748","display_name":"Kai Sommer","orcid":"https://orcid.org/0000-0003-1866-8247"},"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":"Kai Sommer","raw_affiliation_strings":["ZBH - Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany"],"affiliations":[{"raw_affiliation_string":"ZBH - Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074582099","display_name":"Pascal Schmidt","orcid":"https://orcid.org/0009-0009-8628-684X"},"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":"Pascal Schmidt","raw_affiliation_strings":["ZBH - Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany"],"affiliations":[{"raw_affiliation_string":"ZBH - Center for Bioinformatics, Universit\u00e4t 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":["ZBH - Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany"],"affiliations":[{"raw_affiliation_string":"ZBH - Center for Bioinformatics, Universit\u00e4t 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":false,"raw_author_name":"Matthias Rarey","raw_affiliation_strings":["ZBH - Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany"],"affiliations":[{"raw_affiliation_string":"ZBH - Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5052571947"],"corresponding_institution_ids":["https://openalex.org/I159176309"],"apc_list":null,"apc_paid":null,"fwci":0.3326,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.53622736,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"57","issue":"9","first_page":"2132","last_page":"2142"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9843000173568726,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9843000173568726,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.968999981880188,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9639999866485596,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/nova","display_name":"Nova (rocket)","score":0.6810827255249023},{"id":"https://openalex.org/keywords/non-covalent-interactions","display_name":"Non-covalent interactions","score":0.5524963140487671},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4393857717514038},{"id":"https://openalex.org/keywords/macromolecule","display_name":"Macromolecule","score":0.4257264733314514},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.32657590508461},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.2717663049697876},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.15915459394454956},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.11437720060348511},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.10258808732032776},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.09780141711235046},{"id":"https://openalex.org/keywords/hydrogen-bond","display_name":"Hydrogen bond","score":0.0804644525051117}],"concepts":[{"id":"https://openalex.org/C199364081","wikidata":"https://www.wikidata.org/wiki/Q183158","display_name":"Nova (rocket)","level":2,"score":0.6810827255249023},{"id":"https://openalex.org/C137277065","wikidata":"https://www.wikidata.org/wiki/Q2915446","display_name":"Non-covalent interactions","level":4,"score":0.5524963140487671},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4393857717514038},{"id":"https://openalex.org/C204389451","wikidata":"https://www.wikidata.org/wiki/Q178593","display_name":"Macromolecule","level":2,"score":0.4257264733314514},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.32657590508461},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.2717663049697876},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.15915459394454956},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.11437720060348511},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.10258808732032776},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.09780141711235046},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.0804644525051117},{"id":"https://openalex.org/C178802073","wikidata":"https://www.wikidata.org/wiki/Q8421","display_name":"Aeronautics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","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":"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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D046911","descriptor_name":"Macromolecular Substances","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D046911","descriptor_name":"Macromolecular Substances","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D046911","descriptor_name":"Macromolecular Substances","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D046911","descriptor_name":"Macromolecular Substances","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046911","descriptor_name":"Macromolecular Substances","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046911","descriptor_name":"Macromolecular Substances","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.7b00291","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.7b00291","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:28891648","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28891648","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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332735","display_name":"Bayer CropScience","ror":"https://ror.org/04hmn8g73"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W1533988144","https://openalex.org/W1975147762","https://openalex.org/W1980337077","https://openalex.org/W1982885147","https://openalex.org/W1987535385","https://openalex.org/W1992632082","https://openalex.org/W1998634168","https://openalex.org/W1999820454","https://openalex.org/W2000061529","https://openalex.org/W2010929249","https://openalex.org/W2023174745","https://openalex.org/W2025667580","https://openalex.org/W2032842297","https://openalex.org/W2046221309","https://openalex.org/W2049663171","https://openalex.org/W2053792165","https://openalex.org/W2064622842","https://openalex.org/W2069739744","https://openalex.org/W2069917705","https://openalex.org/W2071407989","https://openalex.org/W2075676398","https://openalex.org/W2081242643","https://openalex.org/W2100598991","https://openalex.org/W2104722869","https://openalex.org/W2106466007","https://openalex.org/W2109720065","https://openalex.org/W2114162221","https://openalex.org/W2130479394","https://openalex.org/W2238707319","https://openalex.org/W2293883304","https://openalex.org/W2315506771","https://openalex.org/W2394923207","https://openalex.org/W2395439412","https://openalex.org/W2466124122","https://openalex.org/W2582406409","https://openalex.org/W2614021444"],"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/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487","https://openalex.org/W1986764834"],"abstract_inverted_index":{"Noncovalent":[0],"interactions":[1,13,73,225],"play":[2],"an":[3,166],"important":[4],"role":[5],"in":[6,32,142,150,162,226],"macromolecular":[7],"complexes.":[8],"The":[9,83,119],"assessment":[10],"of":[11,51,59,71,80,108,117,127,159,165,172,208,223],"molecular":[12,81],"is":[14,85,230],"often":[15],"based":[16],"on":[17,22,169],"knowledge":[18],"derived":[19],"from":[20,175],"statistics":[21,110],"structural":[23],"data.":[24],"Within":[25],"the":[26,29,33,49,69,78,93,99,106,114,124,163,190,204],"last":[27],"years,":[28],"available":[30,231],"data":[31,60,140],"Brookhaven":[34],"Protein":[35],"Data":[36],"Bank":[37],"has":[38],"increased":[39],"dramatically,":[40],"quantitatively":[41],"as":[42,44,121,123],"well":[43,122],"qualitatively.":[45],"This":[46],"development":[47],"allows":[48,105],"derivation":[50],"enhanced":[52],"interaction":[53],"models":[54],"and":[55,211],"motivates":[56],"new":[57],"ways":[58],"analysis.":[61],"Here,":[62],"we":[63,202],"present":[64,203],"a":[65,88,160,170,176,180],"method":[66,84,210],"to":[67,95,113,219],"facilitate":[68],"analysis":[70,158,222],"noncovalent":[72,224],"enabling":[74,92],"detailed":[75],"insights":[76],"into":[77,87],"nature":[79],"interactions.":[82],"integrated":[86],"highly":[89],"variable":[90],"framework":[91],"adaption":[94],"user-specific":[96],"requirements.":[97],"NAOMInova,":[98],"user":[100],"interface":[101],"for":[102,139,156,182,196],"our":[103,209],"method,":[104],"generation":[107],"specific":[109],"with":[111,152],"respect":[112],"chemical":[115],"environment":[116],"substructures.":[118],"substructures":[120],"analyzed":[125],"set":[126,171],"protein":[128,227],"structures":[129,173],"can":[130,147,186],"be":[131,148,187],"chosen":[132],"arbitrarily.":[133],"Although":[134],"NAOMInova":[135,229],"was":[136],"primarily":[137],"made":[138],"exploration":[141],"protein-ligand":[143],"crystal":[144],"structures,":[145],"it":[146],"used":[149],"combination":[151],"any":[153],"structure":[154],"collection,":[155],"example,":[157],"carbonyl":[161],"neighborhood":[164],"aromatic":[167],"ring":[168],"resulting":[174],"MD":[177],"simulation.":[178],"Additionally,":[179],"filter":[181],"different":[183],"atom":[184],"attributes":[185],"applied":[188],"including":[189],"experimental":[191],"support":[192,220],"by":[193],"electron":[194],"density":[195],"single":[197],"atoms.":[198],"In":[199],"this":[200],"publication,":[201],"underlying":[205],"algorithmic":[206],"techniques":[207],"show":[212],"application":[213],"examples":[214],"that":[215],"demonstrate":[216],"NAOMInova's":[217],"ability":[218],"individual":[221],"structures.":[228],"at":[232],"http://www.zbh.uni-hamburg.de/naominova":[233],".":[234]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2017-09-25T00:00:00"}
