{"id":"https://openalex.org/W2108452336","doi":"https://doi.org/10.1093/bioinformatics/btv416","title":"RxnSim: a tool to compare biochemical reactions","display_name":"RxnSim: a tool to compare biochemical reactions","publication_year":2015,"publication_date":"2015-07-17","ids":{"openalex":"https://openalex.org/W2108452336","doi":"https://doi.org/10.1093/bioinformatics/btv416","mag":"2108452336","pmid":"https://pubmed.ncbi.nlm.nih.gov/26187943"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv416","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv416","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5064039422","display_name":"Varun Giri","orcid":"https://orcid.org/0000-0001-6055-6324"},"institutions":[{"id":"https://openalex.org/I4210139030","display_name":"Samsung (India)","ror":"https://ror.org/04cpx2569","country_code":"IN","type":"company","lineage":["https://openalex.org/I2250650973","https://openalex.org/I4210139030"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Varun Giri","raw_affiliation_strings":["1 Bioinformatics Lab, Samsung Advanced Institute of Technology, Bangalore 560037, India and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Bioinformatics Lab, Samsung Advanced Institute of Technology, Bangalore 560037, India and","institution_ids":["https://openalex.org/I4210139030"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Tadi Venkata Sivakumar","orcid":null},"institutions":[{"id":"https://openalex.org/I4210139030","display_name":"Samsung (India)","ror":"https://ror.org/04cpx2569","country_code":"IN","type":"company","lineage":["https://openalex.org/I2250650973","https://openalex.org/I4210139030"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Tadi Venkata Sivakumar","raw_affiliation_strings":["1 Bioinformatics Lab, Samsung Advanced Institute of Technology, Bangalore 560037, India and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Bioinformatics Lab, Samsung Advanced Institute of Technology, Bangalore 560037, India and","institution_ids":["https://openalex.org/I4210139030"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111950830","display_name":"Kwang Myung Cho","orcid":null},"institutions":[{"id":"https://openalex.org/I2250650973","display_name":"Samsung (South Korea)","ror":"https://ror.org/04w3jy968","country_code":"KR","type":"company","lineage":["https://openalex.org/I2250650973"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Kwang Myung Cho","raw_affiliation_strings":["2 Biomaterials Lab, Materials Center, Samsung Advanced Institute of Technology, Gyeonggi-do 443803, Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Biomaterials Lab, Materials Center, Samsung Advanced Institute of Technology, Gyeonggi-do 443803, Korea","institution_ids":["https://openalex.org/I2250650973"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047156899","display_name":"Tae Yong Kim","orcid":"https://orcid.org/0000-0003-4982-4441"},"institutions":[{"id":"https://openalex.org/I2250650973","display_name":"Samsung (South Korea)","ror":"https://ror.org/04w3jy968","country_code":"KR","type":"company","lineage":["https://openalex.org/I2250650973"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Tae Yong Kim","raw_affiliation_strings":["2 Biomaterials Lab, Materials Center, Samsung Advanced Institute of Technology, Gyeonggi-do 443803, Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Biomaterials Lab, Materials Center, Samsung Advanced Institute of Technology, Gyeonggi-do 443803, Korea","institution_ids":["https://openalex.org/I2250650973"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028699541","display_name":"Anirban Bhaduri","orcid":"https://orcid.org/0000-0002-7787-3550"},"institutions":[{"id":"https://openalex.org/I4210139030","display_name":"Samsung (India)","ror":"https://ror.org/04cpx2569","country_code":"IN","type":"company","lineage":["https://openalex.org/I2250650973","https://openalex.org/I4210139030"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Anirban Bhaduri","raw_affiliation_strings":["1 Bioinformatics Lab, Samsung Advanced Institute of Technology, Bangalore 560037, India and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Bioinformatics Lab, Samsung Advanced Institute of Technology, Bangalore 560037, India and","institution_ids":["https://openalex.org/I4210139030"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5028699541","https://openalex.org/A5047156899"],"corresponding_institution_ids":["https://openalex.org/I2250650973","https://openalex.org/I4210139030"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.9713,"has_fulltext":false,"cited_by_count":24,"citation_normalized_percentile":{"value":0.74862242,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"31","issue":"22","first_page":"3712","last_page":"3714"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.3255000114440918,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.3255000114440918,"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":0.15330000221729279,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.1160999983549118,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7154752016067505},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.6981439590454102},{"id":"https://openalex.org/keywords/chemical-similarity","display_name":"Chemical similarity","score":0.5959757566452026},{"id":"https://openalex.org/keywords/transformation","display_name":"Transformation (genetics)","score":0.5775974988937378},{"id":"https://openalex.org/keywords/chemical-database","display_name":"Chemical database","score":0.5632113814353943},{"id":"https://openalex.org/keywords/masking","display_name":"Masking (illustration)","score":0.5082702040672302},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.48808348178863525},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4631110727787018},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.369348406791687},{"id":"https://openalex.org/keywords/structural-similarity","display_name":"Structural similarity","score":0.3116842210292816},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.21469047665596008},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.20750361680984497},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15704715251922607},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.06374749541282654}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7154752016067505},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.6981439590454102},{"id":"https://openalex.org/C24259465","wikidata":"https://www.wikidata.org/wiki/Q2272153","display_name":"Chemical similarity","level":3,"score":0.5959757566452026},{"id":"https://openalex.org/C204241405","wikidata":"https://www.wikidata.org/wiki/Q461499","display_name":"Transformation (genetics)","level":3,"score":0.5775974988937378},{"id":"https://openalex.org/C203394866","wikidata":"https://www.wikidata.org/wiki/Q2881060","display_name":"Chemical database","level":2,"score":0.5632113814353943},{"id":"https://openalex.org/C2777402240","wikidata":"https://www.wikidata.org/wiki/Q6783436","display_name":"Masking (illustration)","level":2,"score":0.5082702040672302},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.48808348178863525},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4631110727787018},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.369348406791687},{"id":"https://openalex.org/C139489369","wikidata":"https://www.wikidata.org/wiki/Q770846","display_name":"Structural similarity","level":2,"score":0.3116842210292816},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.21469047665596008},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.20750361680984497},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15704715251922607},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.06374749541282654},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062126","descriptor_name":"Databases, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062126","descriptor_name":"Databases, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062126","descriptor_name":"Databases, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btv416","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv416","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26187943","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26187943","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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:31/22/3712","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/22/3712","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.4099999964237213,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332195","display_name":"Samsung","ror":"https://ror.org/04w3jy968"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W1605923270","https://openalex.org/W1862448690","https://openalex.org/W1976439126","https://openalex.org/W1996830618","https://openalex.org/W2060586571","https://openalex.org/W2064576005","https://openalex.org/W2082593499","https://openalex.org/W2095279025","https://openalex.org/W2096729078","https://openalex.org/W2103612757","https://openalex.org/W2119512897","https://openalex.org/W2125117729","https://openalex.org/W2126097199","https://openalex.org/W2136869178","https://openalex.org/W2166138679"],"related_works":["https://openalex.org/W1987966112","https://openalex.org/W4292296636","https://openalex.org/W358917076","https://openalex.org/W2090768198","https://openalex.org/W1996722392","https://openalex.org/W2042007894","https://openalex.org/W22579956","https://openalex.org/W2007239199","https://openalex.org/W4255337529","https://openalex.org/W3042279869"],"abstract_inverted_index":{"UNLABELLED:":[0],":":[1],"Quantitative":[2],"assessment":[3],"of":[4,12,16,43,56,68],"chemical":[5,26,70],"reaction":[6,22,36],"similarity":[7,23,37,74],"aids":[8],"database":[9],"searches,":[10],"classification":[11],"reactions":[13,52],"and":[14,58,84],"identification":[15],"candidate":[17],"enzymes.":[18],"Most":[19],"methods":[20],"evaluate":[21],"based":[24,38,53],"on":[25,39,54],"transformation":[27],"patterns.":[28],"We":[29],"describe":[30],"a":[31],"tool,":[32],"RxnSim,":[33],"which":[34],"computes":[35],"the":[40,89],"molecular":[41],"signatures":[42],"participating":[44],"molecules.":[45],"The":[46],"tool":[47],"is":[48,80,85],"able":[49],"to":[50,62],"compare":[51],"similarities":[55],"substrates":[57],"products":[59],"in":[60,82],"addition":[61],"their":[63],"transformation.":[64],"It":[65],"allows":[66],"masking":[67],"user-defined":[69],"moieties":[71],"for":[72],"weighted":[73],"computations.":[75],"AVAILABILITY":[76],"AND":[77],"IMPLEMENTATION:":[78],"RxnSim":[79],"implemented":[81],"R":[83,91],"freely":[86],"available":[87,105],"from":[88],"Comprehensive":[90],"Archive":[92],"Network,":[93],"CRAN":[94],"(http://cran.r-project.org/web/packages/RxnSim/).":[95],"CONTACT:":[96],"anirban.b@samsung.com":[97],"or":[98],"ty76.kim@samsung.com":[99],"SUPPLEMENTARY":[100],"INFORMATION:":[101],"Supplementary":[102],"data":[103],"are":[104],"at":[106],"Bioinformatics":[107],"online.":[108]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":1}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}