{"id":"https://openalex.org/W4385620653","doi":"https://doi.org/10.1021/acs.jcim.3c00890","title":"Rapid and Automated <i>Ab Initio</i> Metabolite Collisional Cross Section Prediction from SMILES Input","display_name":"Rapid and Automated <i>Ab Initio</i> Metabolite Collisional Cross Section Prediction from SMILES Input","publication_year":2023,"publication_date":"2023-08-07","ids":{"openalex":"https://openalex.org/W4385620653","doi":"https://doi.org/10.1021/acs.jcim.3c00890","pmid":"https://pubmed.ncbi.nlm.nih.gov/37548575"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c00890","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00890","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/A5024166110","display_name":"Susanta Das","orcid":"https://orcid.org/0000-0001-7981-5162"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Susanta Das","raw_affiliation_strings":["Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States"],"raw_orcid":"https://orcid.org/0000-0001-7981-5162","affiliations":[{"raw_affiliation_string":"Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047693774","display_name":"Laleh Dinpazhoh","orcid":"https://orcid.org/0000-0003-3220-6700"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Laleh Dinpazhoh","raw_affiliation_strings":["Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003123572","display_name":"Kiyoto Aramis Tanemura","orcid":"https://orcid.org/0000-0002-9084-5976"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kiyoto Aramis Tanemura","raw_affiliation_strings":["Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085994852","display_name":"Kenneth M. Merz","orcid":"https://orcid.org/0000-0001-9139-5893"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kenneth M. Merz","raw_affiliation_strings":["Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States"],"raw_orcid":"https://orcid.org/0000-0001-9139-5893","affiliations":[{"raw_affiliation_string":"Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States","institution_ids":["https://openalex.org/I87216513"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5085994852"],"corresponding_institution_ids":["https://openalex.org/I87216513"],"apc_list":null,"apc_paid":null,"fwci":0.9418,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.75466493,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"63","issue":"16","first_page":"4995","last_page":"5000"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9998000264167786,"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"}},"topics":[{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9998000264167786,"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/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9962999820709229,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"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/T13551","display_name":"Biochemical effects in animals","score":0.994700014591217,"subfield":{"id":"https://openalex.org/subfields/2737","display_name":"Physiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.8425978422164917},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6270327568054199},{"id":"https://openalex.org/keywords/ab-initio","display_name":"Ab initio","score":0.5962134599685669},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5871062278747559},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.49247297644615173},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4692418873310089},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.455163836479187},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.43274733424186707},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.41954949498176575},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38109293580055237},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.22301331162452698},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1974140703678131},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.16450834274291992}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8425978422164917},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6270327568054199},{"id":"https://openalex.org/C2781442258","wikidata":"https://www.wikidata.org/wiki/Q46310","display_name":"Ab initio","level":2,"score":0.5962134599685669},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5871062278747559},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.49247297644615173},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4692418873310089},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.455163836479187},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.43274733424186707},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.41954949498176575},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38109293580055237},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.22301331162452698},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1974140703678131},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.16450834274291992},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009682","descriptor_name":"Magnetic Resonance Spectroscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009682","descriptor_name":"Magnetic Resonance Spectroscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009682","descriptor_name":"Magnetic Resonance Spectroscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.3c00890","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00890","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:37548575","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37548575","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":[{"score":0.5299999713897705,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G2104131143","display_name":null,"funder_award_id":"1U2CES030167-01","funder_id":"https://openalex.org/F4320338403","funder_display_name":"Common Fund"},{"id":"https://openalex.org/G2514423481","display_name":null,"funder_award_id":"U2C ES030167","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"}],"funders":[{"id":"https://openalex.org/F4320337361","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63"},{"id":"https://openalex.org/F4320338403","display_name":"Common Fund","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1965038686","https://openalex.org/W2125069590","https://openalex.org/W2135378461","https://openalex.org/W2158219301","https://openalex.org/W2244785476","https://openalex.org/W2333743632","https://openalex.org/W2755377387","https://openalex.org/W2792854094","https://openalex.org/W2911354688","https://openalex.org/W2920724574","https://openalex.org/W2925495008","https://openalex.org/W2982596783","https://openalex.org/W3033054884","https://openalex.org/W3034390843","https://openalex.org/W3035839386","https://openalex.org/W3040650539","https://openalex.org/W3082061703","https://openalex.org/W3098953572","https://openalex.org/W3146454937","https://openalex.org/W3160644197","https://openalex.org/W4210644165","https://openalex.org/W4226016500"],"related_works":["https://openalex.org/W1981780420","https://openalex.org/W2182707996","https://openalex.org/W45233828","https://openalex.org/W2964988449","https://openalex.org/W188202134","https://openalex.org/W2397952901","https://openalex.org/W2029380707","https://openalex.org/W4255934811","https://openalex.org/W2465382974","https://openalex.org/W2088034942"],"abstract_inverted_index":{"CCS":[0,55,89,117],"prediction":[1,148],"workflow":[2,106,138],"which":[3,69,142],"incrementally":[4],"refines":[5],"generated":[6],"structures":[7],"using":[8],"molecular":[9,58],"mechanics,":[10],"a":[11,25,44,57,61,80,99],"deep":[12],"learning":[13],"potential,":[14],"conformational":[15],"clustering,":[16],"and":[17,42,113],"quantum":[18],"mechanics":[19],"(QM).":[20],"Automating":[21],"intermediate":[22,140],"steps":[23,109],"for":[24,122,136,146],"high":[26],"performance":[27],"computing":[28],"(HPC)":[29],"environment":[30],"allows":[31],"users":[32],"to":[33],"input":[34],"the":[35,88,93,105,115,131,137,147,167],"SMILES":[36],"structure":[37],"of":[38,56,73,149],"small":[39],"organic":[40],"molecules":[41],"obtain":[43],"Boltzmann":[45],"averaged":[46],"collisional":[47],"cross":[48],"section":[49],"(CCS)":[50],"value":[51,118],"as":[52,153],"output.":[53],"The":[54,162],"species":[59],"is":[60,164],"metric":[62],"measured":[63],"by":[64,91],"ion":[65],"mobility":[66],"spectrometry":[67],"(IMS)":[68],"can":[70,143],"improve":[71],"annotation":[72],"untargeted":[74],"metabolomics":[75],"experiments.":[76],"We":[77],"report":[78],"only":[79],"minor":[81],"drop":[82],"in":[83],"accuracy":[84],"when":[85],"we":[86,128],"expedite":[87],"calculation":[90],"replacing":[92],"QM":[94],"geometry":[95],"refinement":[96],"step":[97],"with":[98],"single-point":[100],"energy":[101],"calculation.":[102],"Even":[103],"though":[104],"involves":[107],"stochastic":[108],"(i.e.,":[110],"conformation":[111],"generation":[112],"clustering),":[114],"final":[116],"was":[119],"highly":[120],"reproducible":[121],"multiple":[123],"iterations":[124],"on":[125],"L-carnosine.":[126],"Finally,":[127],"illustrate":[129],"that":[130],"gas":[132],"phase":[133,155],"ensembles":[134],"modeled":[135],"are":[139],"files":[141],"be":[144],"used":[145],"other":[150],"properties":[151],"such":[152],"aqueous":[154],"nuclear":[156],"magnetic":[157],"resonance":[158],"chemical":[159],"shift":[160],"prediction.":[161],"software":[163],"available":[165],"at":[166],"following":[168],"link:":[169],"https://github.com/DasSusanta/snakemake_ccs.":[170]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}
