{"id":"https://openalex.org/W2524455268","doi":"https://doi.org/10.1186/s13321-016-0160-4","title":"Jmol SMILES and Jmol SMARTS: specifications and applications","display_name":"Jmol SMILES and Jmol SMARTS: specifications and applications","publication_year":2016,"publication_date":"2016-09-26","ids":{"openalex":"https://openalex.org/W2524455268","doi":"https://doi.org/10.1186/s13321-016-0160-4","mag":"2524455268","pmid":"https://pubmed.ncbi.nlm.nih.gov/28316648"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-016-0160-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-016-0160-4","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-016-0160-4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-016-0160-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054098999","display_name":"Robert M. Hanson","orcid":"https://orcid.org/0000-0001-5411-2356"},"institutions":[{"id":"https://openalex.org/I24861097","display_name":"St. Olaf College","ror":"https://ror.org/01q7w1f47","country_code":"US","type":"education","lineage":["https://openalex.org/I24861097"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Robert M. Hanson","raw_affiliation_strings":["Department of Chemistry, St. Olaf College, 1520 St. Olaf Ave., Northfield, MN USA","Department of Chemistry, St. Olaf College, 1520 St. Olaf Ave., Northfield, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, St. Olaf College, 1520 St. Olaf Ave., Northfield, MN USA","institution_ids":["https://openalex.org/I24861097"]},{"raw_affiliation_string":"Department of Chemistry, St. Olaf College, 1520 St. Olaf Ave., Northfield, MN, USA","institution_ids":["https://openalex.org/I24861097"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5054098999"],"corresponding_institution_ids":["https://openalex.org/I24861097"],"apc_list":{"value":2390,"currency":"USD","value_usd":2390},"apc_paid":{"value":2390,"currency":"USD","value_usd":2390},"fwci":1.3301,"has_fulltext":true,"cited_by_count":54,"citation_normalized_percentile":{"value":0.79440487,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"8","issue":"1","first_page":"50","last_page":"50"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.40209999680519104,"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":0.40209999680519104,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.1956000030040741,"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/T12748","display_name":"Molecular spectroscopy and chirality","score":0.06710000336170197,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.674730658531189}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.674730658531189}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/s13321-016-0160-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-016-0160-4","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-016-0160-4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:28316648","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28316648","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 cheminformatics","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:4205336","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5037863","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-016-0160-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-016-0160-4","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-016-0160-4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2524455268.pdf","grobid_xml":"https://content.openalex.org/works/W2524455268.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W255996521","https://openalex.org/W1243254526","https://openalex.org/W1534928504","https://openalex.org/W1975147762","https://openalex.org/W1993267444","https://openalex.org/W1998997530","https://openalex.org/W2029667189","https://openalex.org/W2037109408","https://openalex.org/W2049654081","https://openalex.org/W2120869341","https://openalex.org/W2132629607","https://openalex.org/W2147085530","https://openalex.org/W2147421370","https://openalex.org/W2172216479","https://openalex.org/W2205915548","https://openalex.org/W2269194472","https://openalex.org/W2951811035"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"BACKGROUND:":[0],"SMILES":[1,57,90,117,174,197,210,222,230,257,268],"and":[2,25,31,36,58,67,76,87,102,122,130,151,161,175,199,211,223,231,258,291,304],"SMARTS":[3,59,135,176,200,212,225,260],"are":[4,79,213,309],"two":[5],"well-defined":[6],"structure":[7],"matching":[8,157,189],"languages":[9],"that":[10,60,64,109],"have":[11,235],"gained":[12],"wide":[13],"use":[14,179],"in":[15,29,33,180,239,249,252,286],"cheminformatics.":[16],"Jmol":[17,49,89,134,217,221,224,253,256,259],"is":[18,91,167],"a":[19,92,97,124,146,185],"widely":[20],"used":[21,294],"open-source":[22],"molecular":[23,159,182,195],"visualization":[24],"analysis":[26],"tool":[27],"written":[28],"Java":[30,35],"implemented":[32],"both":[34],"JavaScript.":[37],"Over":[38],"the":[39,52,104,111,171,216],"past":[40],"10":[41],"years,":[42],"from":[43,243,281,312],"2007":[44],"to":[45,141,156,228,295],"2016,":[46],"work":[47],"on":[48],"has":[50],"included":[51],"development":[53],"of":[54,56,73,94,106,113,116,128,148,153,170,173,188,193,209,215,273,278,299],"dialects":[55,82,208],"incorporate":[61],"novel":[62],"aspects":[63,115],"allow":[65],"new":[66],"powerful":[68],"applications.":[69],"RESULTS:":[70],"The":[71,81,165],"specifications":[72],"\"Jmol":[74,77],"SMILES\"":[75],"SMARTS\"":[78],"described.":[80],"most":[83],"closely":[84],"resemble":[85],"OpenSMILES":[86],"OpenSMARTS.":[88],"superset":[93],"OpenSMILES,":[95],"allowing":[96,184],"freer":[98],"format,":[99],"including":[100],"whitespace":[101],"comments,":[103],"addition":[105],"\"processing":[107],"directives\"":[108],"modify":[110],"meaning":[112],"certain":[114],"processing":[118],"such":[119],"as":[120,247],"aromaticity":[121],"stereochemistry,":[123,129],"more":[125],"extensive":[126],"treatment":[127],"several":[131],"minor":[132],"additions.":[133],"similarly":[136],"adds":[137,145],"these":[138,207],"same":[139],"modifications":[140],"OpenSMARTS,":[142],"but":[143],"also":[144],"number":[147],"additional":[149],"\"primitives\"":[150],"elements":[152],"syntax":[154],"tuned":[155],"3D":[158,181,194,244,279,302],"structures":[160,280],"selecting":[162],"their":[163],"atoms.":[164],"result":[166],"an":[168],"expansion":[169],"capabilities":[172],"primarily":[177],"for":[178,205],"analysis,":[183],"broader":[186],"range":[187],"involving":[190],"any":[191],"combination":[192],"structures,":[196,301,303],"strings,":[198],"patterns.":[201],"While":[202],"developed":[203],"specifically":[204],"Jmol,":[206],"independent":[214],"application":[218],"itself.":[219],"CONCLUSIONS:":[220],"add":[226],"value":[227],"standard":[229],"SMARTS.":[232],"Together":[233],"they":[234],"proven":[236],"exceptionally":[237],"capable":[238],"extracting":[240],"valuable":[241],"information":[242],"structural":[245],"models,":[246],"demonstrated":[248],"Jmol.":[250],"Capabilities":[251],"enabled":[254],"by":[255],"include":[261],"efficient":[262],"MMFF94":[263],"atom":[264,292],"typing,":[265],"conformational":[266,288],"identification,":[267],"comparisons":[269],"without":[270],"canonicalization,":[271],"identification":[272],"stereochemical":[274],"relationships,":[275],"quantitative":[276],"comparison":[277],"different":[282],"sources":[283],"(including":[284],"differences":[285],"Kekulization),":[287],"flexible":[289],"fitting,":[290],"mapping":[293],"synchronize":[296],"interactive":[297],"displays":[298],"2D":[300],"spectral":[305],"correlations,":[306],"where":[307],"data":[308],"being":[310],"drawn":[311],"multiple":[313],"sources.":[314]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":15},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":4}],"updated_date":"2026-09-02T18:50:13.731487","created_date":"2025-10-10T00:00:00"}