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Literature DB >> 21752802

RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity.

Qian-Nan Hu¹, Zhe Deng, Huanan Hu, Dong-Sheng Cao, Yi-Zeng Liang.

Abstract

SUMMARY: Biochemical reactions play a key role to help sustain life and allow cells to grow. RxnFinder was developed to search biochemical reactions from KEGG reaction database using three search criteria: molecular structures, molecular fragments and reaction similarity. RxnFinder is helpful to get reference reactions for biosynthesis and xenobiotics metabolism. AVAILABILITY: RxnFinder is freely available via: http://sdd.whu.edu.cn/rxnfinder. CONTACT: qnhu@whu.edu.cn.

Mesh：

Year: 2011 PMID： 21752802 DOI： 10.1093/bioinformatics/btr413

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

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Cited

12 in total

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Journal: Nucleic Acids Res Date: 2020-07-02 Impact factor: 16.971

2. Methylglucosylation of aromatic amino and phenolic moieties of drug-like biosynthons by combinatorial biosynthesis.

Authors: Linan Xie; Liwen Zhang; Chen Wang; Xiaojing Wang; Ya-Ming Xu; Hefen Yu; Ping Wu; Shenglan Li; Lida Han; A A Leslie Gunatilaka; Xiaoyi Wei; Min Lin; István Molnár; Yuquan Xu
Journal: Proc Natl Acad Sci U S A Date: 2018-05-14 Impact factor: 11.205

3. A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks.

Authors: Hojung Nam; Miguel Campodonico; Aarash Bordbar; Daniel R Hyduke; Sangwoo Kim; Daniel C Zielinski; Bernhard O Palsson
Journal: PLoS Comput Biol Date: 2014-09-18 Impact factor: 4.475

4. A systems biology approach reveals the dose- and time-dependent effect of primary human airway epithelium tissue culture after exposure to cigarette smoke in vitro.

Authors: Carole Mathis; Stephan Gebel; Carine Poussin; Vincenzo Belcastro; Alain Sewer; Dirk Weisensee; Arnd Hengstermann; Sam Ansari; Sandra Wagner; Manuel C Peitsch; Julia Hoeng
Journal: Bioinform Biol Insights Date: 2015-03-09

RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity.

1. novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model.

2. Methylglucosylation of aromatic amino and phenolic moieties of drug-like biosynthons by combinatorial biosynthesis.

3. A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks.

4. A systems biology approach reveals the dose- and time-dependent effect of primary human airway epithelium tissue culture after exposure to cigarette smoke in vitro.

5. Chemical reaction vector embeddings: towards predicting drug metabolism in the human gut microbiome.

6. Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites.

7. Assignment of EC numbers to enzymatic reactions with reaction difference fingerprints.

8. VNP: Interactive Visual Network Pharmacology of Diseases, Targets, and Drugs.

Review 9. A review of computational tools for design and reconstruction of metabolic pathways.

10. SimCAL: a flexible tool to compute biochemical reaction similarity.