{"id":"https://openalex.org/W3011894284","doi":"https://doi.org/10.1021/acs.jcim.0c00025","title":"Improving Conformer Generation for Small Rings and Macrocycles Based on Distance Geometry and Experimental Torsional-Angle Preferences","display_name":"Improving Conformer Generation for Small Rings and Macrocycles Based on Distance Geometry and Experimental Torsional-Angle Preferences","publication_year":2020,"publication_date":"2020-03-10","ids":{"openalex":"https://openalex.org/W3011894284","doi":"https://doi.org/10.1021/acs.jcim.0c00025","mag":"3011894284","pmid":"https://pubmed.ncbi.nlm.nih.gov/32155061"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.0c00025","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00025","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.0c00025","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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","datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.0c00025","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082747737","display_name":"Shuzhe Wang","orcid":"https://orcid.org/0000-0001-7543-7387"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Shuzhe Wang","raw_affiliation_strings":["Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland"],"raw_orcid":"https://orcid.org/0000-0001-7543-7387","affiliations":[{"raw_affiliation_string":"Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060807124","display_name":"Jagna Witek","orcid":"https://orcid.org/0000-0003-1476-6130"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Jagna Witek","raw_affiliation_strings":["Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056808182","display_name":"Gregory A. Landrum","orcid":"https://orcid.org/0000-0001-6279-4481"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gregory A. Landrum","raw_affiliation_strings":["T5 Informatics GmbH, Spalenring 11, 4055 Basel, Switzerland"],"raw_orcid":"https://orcid.org/0000-0001-6279-4481","affiliations":[{"raw_affiliation_string":"T5 Informatics GmbH, Spalenring 11, 4055 Basel, Switzerland","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019754904","display_name":"Sereina Riniker","orcid":"https://orcid.org/0000-0003-1893-4031"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Sereina Riniker","raw_affiliation_strings":["Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland"],"raw_orcid":"https://orcid.org/0000-0003-1893-4031","affiliations":[{"raw_affiliation_string":"Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5019754904"],"corresponding_institution_ids":["https://openalex.org/I35440088"],"apc_list":null,"apc_paid":null,"fwci":14.7176,"has_fulltext":false,"cited_by_count":243,"citation_normalized_percentile":{"value":0.99137357,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"60","issue":"4","first_page":"2044","last_page":"2058"},"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9966999888420105,"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/T10798","display_name":"Crystallography and molecular interactions","score":0.9937000274658203,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/conformational-isomerism","display_name":"Conformational isomerism","score":0.8912924528121948},{"id":"https://openalex.org/keywords/generator","display_name":"Generator (circuit theory)","score":0.5200566649436951},{"id":"https://openalex.org/keywords/cheminformatics","display_name":"Cheminformatics","score":0.5197145938873291},{"id":"https://openalex.org/keywords/small-molecule","display_name":"Small molecule","score":0.49754050374031067},{"id":"https://openalex.org/keywords/heuristics","display_name":"Heuristics","score":0.48163145780563354},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.46846291422843933},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.46158555150032043},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4236214756965637},{"id":"https://openalex.org/keywords/sampling","display_name":"Sampling (signal processing)","score":0.41112980246543884},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3728211522102356},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.37193137407302856},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.3105955421924591},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2222873866558075},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.19684970378875732},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.0826827883720398}],"concepts":[{"id":"https://openalex.org/C18705241","wikidata":"https://www.wikidata.org/wiki/Q1128023","display_name":"Conformational isomerism","level":3,"score":0.8912924528121948},{"id":"https://openalex.org/C2780992000","wikidata":"https://www.wikidata.org/wiki/Q17016113","display_name":"Generator (circuit theory)","level":3,"score":0.5200566649436951},{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.5197145938873291},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.49754050374031067},{"id":"https://openalex.org/C127705205","wikidata":"https://www.wikidata.org/wiki/Q5748245","display_name":"Heuristics","level":2,"score":0.48163145780563354},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.46846291422843933},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.46158555150032043},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4236214756965637},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.41112980246543884},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3728211522102356},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.37193137407302856},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3105955421924591},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2222873866558075},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.19684970378875732},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0826827883720398},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C163258240","wikidata":"https://www.wikidata.org/wiki/Q25342","display_name":"Power (physics)","level":2,"score":0.0},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","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}],"mesh":[{"descriptor_ui":"D000066506","descriptor_name":"Heuristics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000066506","descriptor_name":"Heuristics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000066506","descriptor_name":"Heuristics","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":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":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jcim.0c00025","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00025","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.0c00025","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:32155061","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32155061","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:www.research-collection.ethz.ch:20.500.11850/414961","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/414961","pdf_url":null,"source":{"id":"https://openalex.org/S4306402302","display_name":"Repository for Publications and Research Data (ETH Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I35440088","host_organization_name":"ETH Zurich","host_organization_lineage":["https://openalex.org/I35440088"],"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":"Journal of Chemical Information and Modeling, 60 (4)","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"doi:10.3929/ethz-b-000414961","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-b-000414961","pdf_url":null,"source":{"id":"https://openalex.org/S7407051236","display_name":"ETH Z\u00fcrich Research Collection","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.0c00025","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00025","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.0c00025","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/16","score":0.6600000262260437,"display_name":"Peace, Justice and strong institutions"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3011894284.pdf"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W1969585025","https://openalex.org/W1983194490","https://openalex.org/W1988219803","https://openalex.org/W1995808589","https://openalex.org/W1995850373","https://openalex.org/W1996295408","https://openalex.org/W2026692111","https://openalex.org/W2039485495","https://openalex.org/W2052818547","https://openalex.org/W2072537419","https://openalex.org/W2078145018","https://openalex.org/W2078374001","https://openalex.org/W2080742476","https://openalex.org/W2086106287","https://openalex.org/W2090431249","https://openalex.org/W2094278785","https://openalex.org/W2094622291","https://openalex.org/W2127790232","https://openalex.org/W2136623753","https://openalex.org/W2147122257","https://openalex.org/W2147988069","https://openalex.org/W2148950790","https://openalex.org/W2157296083","https://openalex.org/W2168008491","https://openalex.org/W2200866600","https://openalex.org/W2234248612","https://openalex.org/W2244785476","https://openalex.org/W2271736303","https://openalex.org/W2319902168","https://openalex.org/W2335897173","https://openalex.org/W2346205968","https://openalex.org/W2473618562","https://openalex.org/W2484160537","https://openalex.org/W2587816047","https://openalex.org/W2596982648","https://openalex.org/W2605040111","https://openalex.org/W2623294445","https://openalex.org/W2726184500","https://openalex.org/W2739232261","https://openalex.org/W2754199378","https://openalex.org/W2761273232","https://openalex.org/W2771905959","https://openalex.org/W2788873578","https://openalex.org/W2789059526","https://openalex.org/W2892816095","https://openalex.org/W2898021236","https://openalex.org/W2900679761","https://openalex.org/W2911847761","https://openalex.org/W2921492615","https://openalex.org/W2942566598","https://openalex.org/W2947947035","https://openalex.org/W2949223833","https://openalex.org/W4211131356"],"related_works":["https://openalex.org/W1573015311","https://openalex.org/W2023036309","https://openalex.org/W2889938001","https://openalex.org/W4386509167","https://openalex.org/W3165034028","https://openalex.org/W1972863456","https://openalex.org/W1570419641","https://openalex.org/W4293771607","https://openalex.org/W2089371831","https://openalex.org/W2319692855"],"abstract_inverted_index":{"The":[0,144,161],"conformer":[1,40,107],"generator":[2],"ETKDG":[3,37,149],"is":[4,96,150],"a":[5,104],"stochastic":[6],"search":[7,117],"method":[8],"that":[9],"utilizes":[10],"distance":[11],"geometry":[12,137],"together":[13],"with":[14],"knowledge":[15],"derived":[16],"from":[17],"experimental":[18],"crystal":[19],"structures.":[20,129],"It":[21],"has":[22],"been":[23],"shown":[24],"to":[25,38,59,73,81,94,114],"generate":[26],"good":[27],"conformers":[28],"for":[29,70,100,106],"acyclic,":[30],"flexible":[31],"molecules.":[32],"This":[33],"work":[34],"builds":[35],"on":[36,152],"improve":[39],"generation":[41],"of":[42,77,85,87,89,119,135,146,155,172],"molecules":[43],"containing":[44],"small":[45,61,101],"or":[46],"large":[47],"aliphatic":[48,62],"(i.e.,":[49],"non-aromatic)":[50],"rings.":[51],"For":[52],"one,":[53],"we":[54,131],"devise":[55],"additional":[56],"torsional-angle":[57],"potentials":[58,69],"describe":[60],"rings":[63],"and":[64,121,138,158],"adapt":[65],"the":[66,75,82,91,116,123,133,147,169,173],"previously":[67],"developed":[68,163],"acyclic":[71],"bonds":[72],"facilitate":[74],"sampling":[76,124],"macrocycles.":[78],"However,":[79],"due":[80],"larger":[83],"number":[84],"degrees":[86],"freedom":[88],"macrocycles,":[90],"conformational":[92],"space":[93,118],"sample":[95],"much":[97],"broader":[98],"than":[99],"molecules,":[102],"creating":[103],"challenge":[105],"generators.":[108],"We":[109],"therefore":[110],"introduce":[111],"different":[112],"heuristics":[113],"restrict":[115],"macrocycles":[120,157],"bias":[122],"toward":[125],"more":[126],"experimentally":[127],"relevant":[128],"Specifically,":[130],"show":[132],"usage":[134],"elliptical":[136],"customizable":[139],"Coulombic":[140],"interactions":[141],"as":[142],"heuristics.":[143],"performance":[145],"improved":[148],"demonstrated":[151],"test":[153],"sets":[154],"diverse":[156],"cyclic":[159],"peptides.":[160],"code":[162],"here":[164],"will":[165],"be":[166],"incorporated":[167],"into":[168],"2020.03":[170],"release":[171],"open-source":[174],"cheminformatics":[175],"library":[176],"RDKit.":[177]},"counts_by_year":[{"year":2026,"cited_by_count":29},{"year":2025,"cited_by_count":60},{"year":2024,"cited_by_count":53},{"year":2023,"cited_by_count":30},{"year":2022,"cited_by_count":41},{"year":2021,"cited_by_count":25},{"year":2020,"cited_by_count":5}],"updated_date":"2026-06-16T09:24:06.705377","created_date":"2025-10-10T00:00:00"}