{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:40Z","timestamp":1740185140547,"version":"3.37.3"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2020,1,17]],"date-time":"2020-01-17T00:00:00Z","timestamp":1579219200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2019YFA0904300","2018YFA0900700","2017YFC1601702"],"award-info":[{"award-number":["2019YFA0904300","2018YFA0900700","2017YFC1601702"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31700081","31570092"],"award-info":[{"award-number":["31700081","31570092"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Scientific Research Conditions and Technical Support System Program","award":["ZSYS-016"],"award-info":[{"award-number":["ZSYS-016"]}]},{"name":"CAS STS program","award":["QYZDB-SSW-SMC012"],"award-info":[{"award-number":["QYZDB-SSW-SMC012"]}]},{"name":"International Partnership Program of Chinese Academy of Sciences of China","award":["153D31KYSB20170121"],"award-info":[{"award-number":["153D31KYSB20170121"]}]},{"DOI":"10.13039\/501100006606","name":"Natural Science Foundation of Tianjin","doi-asserted-by":"publisher","award":["15JCYBJC54300"],"award-info":[{"award-number":["15JCYBJC54300"]}],"id":[{"id":"10.13039\/501100006606","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Molecular scaffolds are useful in medicinal chemistry to describe, discuss and visualize series of chemical compounds, biochemical transformations and associated biological properties.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present RxnBLAST as a web-based tool for analyzing scaffold transformations and reactive chemical environment features in bioreactions. RxnBLAST extracts chemical features from bioreactions including atom\u2013atom mapping, reaction centers, rules and functional groups to help understand chemical compositions and reaction patterns. Core-to-Core is proposed, which can be utilized in scaffold networks and for constructing a reaction space, as well as providing guidance for subsequent biosynthesis efforts.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>RxnBLAST is available at: http:\/\/design.rxnfinder.org\/rxnblast\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa036","type":"journal-article","created":{"date-parts":[[2020,1,14]],"date-time":"2020-01-14T12:12:20Z","timestamp":1579003940000},"page":"2946-2947","source":"Crossref","is-referenced-by-count":3,"title":["RxnBLAST: molecular scaffold and reactive chemical environment feature extractor for biochemical reactions"],"prefix":"10.1093","volume":"36","author":[{"given":"Xingxiang","family":"Cheng","sequence":"first","affiliation":[{"name":"CAS Key Laboratory of Computational Biology , CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dandan","family":"Sun","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Computational Biology , CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dachuan","family":"Zhang","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Computational Biology , CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu","family":"Tian","sequence":"additional","affiliation":[{"name":"Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences, Tianjin 300308, China"},{"name":"University of Chinese Academy of Sciences , Beijing 100864, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shaozhen","family":"Ding","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Computational Biology , CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pengli","family":"Cai","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Computational Biology , CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qian-Nan","family":"Hu","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Computational Biology , CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,1,17]]},"reference":[{"key":"2023013111480301600_btaa036-B1","doi-asserted-by":"crossref","first-page":"2887","DOI":"10.1021\/jm9602928","article-title":"The properties of known drugs. 1. Molecular frameworks","volume":"39","author":"Bemis","year":"1996","journal-title":"J. Med. Chem"},{"key":"2023013111480301600_btaa036-B2","doi-asserted-by":"crossref","first-page":"5348","DOI":"10.1002\/anie.200600881","article-title":"The core and most useful molecules in organic chemistry","volume":"45","author":"Bishop","year":"2006","journal-title":"Angew. Chem. Int. Ed"},{"key":"2023013111480301600_btaa036-B3","doi-asserted-by":"crossref","first-page":"1217","DOI":"10.2174\/138955706778742768","article-title":"On scaffolds and hopping in medicinal chemistry","volume":"6","author":"Brown","year":"2006","journal-title":"Mini Rev. Med. Chem"},{"key":"2023013111480301600_btaa036-B4","doi-asserted-by":"crossref","first-page":"7263","DOI":"10.1002\/anie.200502272","article-title":"Architecture and evolution of organic chemistry","volume":"44","author":"Fialkowski","year":"2005","journal-title":"Angew. Chem. Int. Ed"},{"key":"2023013111480301600_btaa036-B5","doi-asserted-by":"crossref","first-page":"6516","DOI":"10.1038\/ncomms7516","article-title":"De novo branching cascades for structural and functional diversity in small molecules","volume":"6","author":"Garcia-Castro","year":"2015","journal-title":"Nat. Commun"},{"key":"2023013111480301600_btaa036-B6","doi-asserted-by":"crossref","first-page":"7586","DOI":"10.1002\/anie.201508818","article-title":"Scaffold diversity synthesis and its application in probe and drug discovery","volume":"55","author":"Garcia-Castro","year":"2016","journal-title":"Angew. Chem. Int. Ed"},{"key":"2023013111480301600_btaa036-B7","doi-asserted-by":"crossref","first-page":"1742","DOI":"10.1021\/ci200179y","article-title":"Lessons learned from molecular scaffold analysis","volume":"51","author":"Hu","year":"2011","journal-title":"J. Chem. Inf. Model"},{"key":"2023013111480301600_btaa036-B8","doi-asserted-by":"crossref","first-page":"D353","DOI":"10.1093\/nar\/gkw1092","article-title":"KEGG: new perspectives on genomes, pathways, diseases and drugs","volume":"45","author":"Kanehisa","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023013111480301600_btaa036-B9","doi-asserted-by":"crossref","first-page":"D415","DOI":"10.1093\/nar\/gkw990","article-title":"Updates in Rhea\u2014an expert curated resource of biochemical reactions","volume":"45","author":"Morgat","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023013111480301600_btaa036-B10","doi-asserted-by":"crossref","first-page":"E1","DOI":"10.3390\/molecules21010001","article-title":"Extended functional groups (EFG): an efficient set for chemical characterization and structure-activity relationship studies of chemical compounds","volume":"21","author":"Salmina","year":"2015","journal-title":"Molecules"},{"key":"2023013111480301600_btaa036-B11","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1186\/s12859-018-2248-5","article-title":"SimCAL: a flexible tool to compute biochemical reaction similarity","volume":"19","author":"Sivakumar","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"2023013111480301600_btaa036-B12","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1038\/nchembio0705-74","article-title":"Diversity-oriented synthesis: exploring the intersections between chemistry and biology","volume":"1","author":"Tan","year":"2005","journal-title":"Nat. Chem. Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa036\/32324223\/btaa036.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/9\/2946\/48983970\/bioinformatics_36_9_2946.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/9\/2946\/48983970\/bioinformatics_36_9_2946.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T20:49:56Z","timestamp":1675198196000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/9\/2946\/5709040"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2020,1,17]]},"references-count":12,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2020,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa036","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2020,5,1]]},"published":{"date-parts":[[2020,1,17]]}}}