{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T12:45:46Z","timestamp":1787661946883,"version":"build-2736575974"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,11,15]]},"abstract":"<jats:p>Motivation: Biochemical pathways engineering is often used to synthesize or degrade target chemicals. In silico screening of the biochemical transformation space allows predicting feasible reactions, constituting these pathways. Current enabling tools are customized to predict reactions based on pre-defined biochemical transformations or reaction rule sets. Reaction rule sets are usually curated manually and tailored to specific applications. They are not exhaustive. In addition, current systems are incapable of regulating and refining data with an aim to tune specificity and sensitivity. A robust and flexible tool that allows automated reaction rule set creation along with regulated pathway prediction and analyses is a need. ReactPRED aims to address the same.<\/jats:p>\n               <jats:p>Results: ReactPRED is an open source flexible and customizable tool enabling users to predict biochemical reactions and pathways. The tool allows automated reaction rule creation from a user defined reaction set. Additionally, reaction rule degree and rule tolerance features allow refinement of predicted data. It is available as a flexible graphical user interface and a console application.<\/jats:p>\n               <jats:p>Availability and implementation: ReactPRED is available at: https:\/\/sourceforge.net\/projects\/reactpred\/.<\/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\/btw491","type":"journal-article","created":{"date-parts":[[2016,8,3]],"date-time":"2016-08-03T02:08:47Z","timestamp":1470190127000},"page":"3522-3524","source":"Crossref","is-referenced-by-count":30,"title":["ReactPRED: a tool to predict and analyze biochemical reactions"],"prefix":"10.1093","volume":"32","author":[{"given":"Tadi Venkata","family":"Sivakumar","sequence":"first","affiliation":[{"name":"1Bioinformatics Lab, Samsung Advanced Institute of Technology, Bangalore 560037, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Varun","family":"Giri","sequence":"additional","affiliation":[{"name":"1Bioinformatics Lab, Samsung Advanced Institute of Technology, Bangalore 560037, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jin Hwan","family":"Park","sequence":"additional","affiliation":[{"name":"2Biomaterials Lab, Materials Center, Samsung Advanced Institute of Technology, Gyeonggi-Do 443803, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tae Yong","family":"Kim","sequence":"additional","affiliation":[{"name":"2Biomaterials Lab, Materials Center, Samsung Advanced Institute of Technology, Gyeonggi-Do 443803, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anirban","family":"Bhaduri","sequence":"additional","affiliation":[{"name":"1Bioinformatics Lab, Samsung Advanced Institute of Technology, Bangalore 560037, India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,8,2]]},"reference":[{"key":"2023020114072617100_btw491-B1","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1093\/bioinformatics\/btu750","article-title":"M-path: a compass for navigating potential metabolic pathways","volume":"31","author":"Araki","year":"2015","journal-title":"Bioinformatics"},{"key":"2023020114072617100_btw491-B2","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/1752-0509-6-10","article-title":"Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms","volume":"6","author":"Carbonell","year":"2012","journal-title":"BMC Syst. 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