{"id":"https://openalex.org/W2613477619","doi":"https://doi.org/10.1021/acs.jcim.6b00614","title":"A Comparison of Quantum and Molecular Mechanical Methods to Estimate Strain Energy in Druglike Fragments","display_name":"A Comparison of Quantum and Molecular Mechanical Methods to Estimate Strain Energy in Druglike Fragments","publication_year":2017,"publication_date":"2017-05-09","ids":{"openalex":"https://openalex.org/W2613477619","doi":"https://doi.org/10.1021/acs.jcim.6b00614","mag":"2613477619","pmid":"https://pubmed.ncbi.nlm.nih.gov/28485585"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.6b00614","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00614","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/A5001650984","display_name":"Benjamin D. Sellers","orcid":"https://orcid.org/0000-0002-4194-1240"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Benjamin D. Sellers","raw_affiliation_strings":["Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States"],"raw_orcid":"https://orcid.org/0000-0002-4194-1240","affiliations":[{"raw_affiliation_string":"Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031490088","display_name":"Natalie C. James","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Natalie C. James","raw_affiliation_strings":["Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022225535","display_name":"Alberto Gobbi","orcid":"https://orcid.org/0000-0003-0434-9237"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Alberto Gobbi","raw_affiliation_strings":["Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5001650984"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":11.0684,"has_fulltext":false,"cited_by_count":95,"citation_normalized_percentile":{"value":0.98550313,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"57","issue":"6","first_page":"1265","last_page":"1275"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10798","display_name":"Crystallography and molecular interactions","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10798","display_name":"Crystallography and molecular interactions","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9980000257492065,"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/T12852","display_name":"Chemical Thermodynamics and Molecular Structure","score":0.9958999752998352,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/strain","display_name":"Strain (injury)","score":0.7381324768066406},{"id":"https://openalex.org/keywords/quantum","display_name":"Quantum","score":0.5451658368110657},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.4505853056907654},{"id":"https://openalex.org/keywords/energy","display_name":"Energy (signal processing)","score":0.41235730051994324},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.364108681678772},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2994549870491028},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.1541096568107605}],"concepts":[{"id":"https://openalex.org/C2778022156","wikidata":"https://www.wikidata.org/wiki/Q576145","display_name":"Strain (injury)","level":2,"score":0.7381324768066406},{"id":"https://openalex.org/C84114770","wikidata":"https://www.wikidata.org/wiki/Q46344","display_name":"Quantum","level":2,"score":0.5451658368110657},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.4505853056907654},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.41235730051994324},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.364108681678772},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2994549870491028},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.1541096568107605},{"id":"https://openalex.org/C105702510","wikidata":"https://www.wikidata.org/wiki/Q514","display_name":"Anatomy","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000081","descriptor_name":"Acetamides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000081","descriptor_name":"Acetamides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000081","descriptor_name":"Acetamides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006841","descriptor_name":"Hydrocarbons, Aromatic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006841","descriptor_name":"Hydrocarbons, Aromatic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006841","descriptor_name":"Hydrocarbons, Aromatic","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"D013314","descriptor_name":"Stress, Mechanical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013314","descriptor_name":"Stress, Mechanical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013314","descriptor_name":"Stress, Mechanical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013844","descriptor_name":"Thiazoles","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013844","descriptor_name":"Thiazoles","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013844","descriptor_name":"Thiazoles","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D055595","descriptor_name":"Mechanical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055595","descriptor_name":"Mechanical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055595","descriptor_name":"Mechanical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.6b00614","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00614","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:28485585","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28485585","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/7","display_name":"Affordable and clean energy","score":0.8999999761581421}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332193","display_name":"Genentech","ror":"https://ror.org/04gndp242"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":50,"referenced_works":["https://openalex.org/W1971275758","https://openalex.org/W1974667766","https://openalex.org/W1975708211","https://openalex.org/W1976106600","https://openalex.org/W1980337077","https://openalex.org/W1981458170","https://openalex.org/W1983401069","https://openalex.org/W1987398924","https://openalex.org/W1989474096","https://openalex.org/W1990627326","https://openalex.org/W1997151511","https://openalex.org/W1997340274","https://openalex.org/W2001428495","https://openalex.org/W2020770089","https://openalex.org/W2021832765","https://openalex.org/W2026090322","https://openalex.org/W2027716126","https://openalex.org/W2037223803","https://openalex.org/W2038827564","https://openalex.org/W2040880581","https://openalex.org/W2044940178","https://openalex.org/W2047730466","https://openalex.org/W2050066735","https://openalex.org/W2057491831","https://openalex.org/W2058363175","https://openalex.org/W2060074735","https://openalex.org/W2067324333","https://openalex.org/W2071123242","https://openalex.org/W2077467665","https://openalex.org/W2078374001","https://openalex.org/W2086505034","https://openalex.org/W2087672213","https://openalex.org/W2090431249","https://openalex.org/W2092930273","https://openalex.org/W2095026430","https://openalex.org/W2095474273","https://openalex.org/W2103784312","https://openalex.org/W2122316177","https://openalex.org/W2127336290","https://openalex.org/W2130479394","https://openalex.org/W2140886907","https://openalex.org/W2143981217","https://openalex.org/W2161482291","https://openalex.org/W2170146596","https://openalex.org/W2222589778","https://openalex.org/W2297564814","https://openalex.org/W2314431251","https://openalex.org/W2319902168","https://openalex.org/W2461433458","https://openalex.org/W3106493598"],"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/W2935759653","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487"],"abstract_inverted_index":{"Reducing":[0],"internal":[1],"strain":[2],"energy":[3,126,140],"in":[4,39],"small":[5],"molecules":[6],"is":[7,136],"critical":[8],"for":[9,185,205],"designing":[10],"potent":[11],"drugs.":[12],"Quantum":[13],"mechanical":[14,18],"(QM)":[15],"and":[16,41,57,80,131,169,194,209,218],"molecular":[17],"(MM)":[19],"methods":[20,34,60,207],"are":[21],"often":[22],"used":[23],"to":[24,31,61,200],"estimate":[25,201],"these":[26],"energies.":[27],"In":[28,114],"an":[29,36],"effort":[30],"determine":[32],"which":[33,165,186],"offer":[35],"optimal":[37],"balance":[38],"accuracy":[40],"performance,":[42],"we":[43,180,210],"have":[44],"carried":[45],"out":[46],"torsion":[47,152],"scan":[48],"analyses":[49],"on":[50,91,154],"62":[51],"fragments.":[52],"We":[53],"compared":[54],"nine":[55],"QM":[56,217],"four":[58],"MM":[59,143,219],"reference":[62],"energies":[63,74,153,193],"calculated":[64,90],"at":[65,84],"a":[66,117,122,129,138],"higher":[67],"level":[68],"of":[69],"theory:":[70],"CCSD(T)/CBS":[71,151],"single":[72,124],"point":[73,125],"(coupled":[75],"cluster":[76],"with":[77,121,167],"single,":[78],"double,":[79],"perturbative":[81],"triple":[82],"excitations":[83],"the":[85,101,145,159,176,190,202,206],"complete":[86],"basis":[87],"set":[88],"limit)":[89],"optimized":[92],"geometries":[93],"using":[94],"MP2/6-311+G**.":[95],"The":[96,192],"results":[97],"show":[98],"that":[99],"both":[100],"more":[102,155],"recent":[103],"MP2.X":[104],"perturbation":[105],"method":[106],"as":[107,109],"well":[108],"MP2/CBS":[110,123],"perform":[111],"quite":[112],"well.":[113],"addition,":[115],"combining":[116],"Hartree-Fock":[118],"geometry":[119],"optimization":[120],"calculation":[127],"offers":[128],"fast":[130],"accurate":[132],"compromise":[133],"when":[134],"dispersion":[135],"not":[137],"key":[139],"component.":[141],"Among":[142],"methods,":[144],"OPLS3":[146,187],"force":[147,163],"field":[148],"accurately":[149],"reproduces":[150],"test":[156],"cases":[157],"than":[158],"MMFF94s":[160],"or":[161],"Amber12:EHT":[162],"fields,":[164],"struggle":[166],"aryl-amide":[168],"aryl-aryl":[170],"torsions.":[171],"Using":[172],"experimental":[173],"conformations":[174,195],"from":[175],"Cambridge":[177],"Structural":[178],"Database,":[179],"highlight":[181],"three":[182],"example":[183],"structures":[184],"significantly":[188],"overestimates":[189],"strain.":[191],"presented":[196],"should":[197],"enable":[198],"scientists":[199],"expected":[203],"error":[204],"described":[208],"hope":[211],"will":[212],"spur":[213],"further":[214],"research":[215],"into":[216],"methods.":[220]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":17},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":16},{"year":2020,"cited_by_count":15},{"year":2019,"cited_by_count":14},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}