{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T09:19:19Z","timestamp":1778059159212,"version":"3.51.4"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary \u00a0: Quantitative assessment of chemical reaction similarity aids database searches, classification of reactions and identification of candidate enzymes. Most methods evaluate reaction similarity based on chemical transformation patterns. We describe a tool, RxnSim, which computes reaction similarity based on the molecular signatures of participating molecules. The tool is able to compare reactions based on similarities of substrates and products in addition to their transformation. It allows masking of user-defined chemical moieties for weighted similarity computations.<\/jats:p>\n               <jats:p>Availability and implementation: RxnSim is implemented in R and is freely available from the Comprehensive R Archive Network, CRAN (http:\/\/cran.r-project.org\/web\/packages\/RxnSim\/).<\/jats:p>\n               <jats:p>Contact: \u00a0anirban.b@samsung.com or ty76.kim@samsung.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv416","type":"journal-article","created":{"date-parts":[[2015,7,18]],"date-time":"2015-07-18T02:16:03Z","timestamp":1437185763000},"page":"3712-3714","source":"Crossref","is-referenced-by-count":22,"title":["RxnSim: a tool to compare biochemical reactions"],"prefix":"10.1093","volume":"31","author":[{"given":"Varun","family":"Giri","sequence":"first","affiliation":[{"name":"1 Bioinformatics Lab, Samsung Advanced Institute of Technology, Bangalore 560037, India and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tadi Venkata","family":"Sivakumar","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Lab, Samsung Advanced Institute of Technology, Bangalore 560037, India and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kwang Myung","family":"Cho","sequence":"additional","affiliation":[{"name":"2 Biomaterials Lab, Materials Center, Samsung Advanced Institute of Technology, Gyeonggi-do 443803, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tae Yong","family":"Kim","sequence":"additional","affiliation":[{"name":"2 Biomaterials Lab, Materials Center, Samsung Advanced Institute of Technology, Gyeonggi-do 443803, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anirban","family":"Bhaduri","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Lab, Samsung Advanced Institute of Technology, Bangalore 560037, India and"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,7,17]]},"reference":[{"key":"2023020202325001000_btv416-B1","doi-asserted-by":"crossref","first-page":"2012","DOI":"10.1093\/bioinformatics\/btq317","article-title":"Molecular signatures-based prediction of enzyme promiscuity","volume":"26","author":"Carbonell","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020202325001000_btv416-B2","doi-asserted-by":"crossref","first-page":"2975","DOI":"10.1093\/bioinformatics\/btp507","article-title":"Metabolite and reaction inference based on enzyme specificities","volume":"25","author":"de Groot","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020202325001000_btv416-B3","doi-asserted-by":"crossref","first-page":"e1000661","DOI":"10.1371\/journal.pcbi.1000661","article-title":"Automated assignment of EC numbers","volume":"6","author":"Egelhofer","year":"2010","journal-title":"PLoS Comput. 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