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Labena AA, Ye YN, Dong C, et al. SSER: Species specific essential reactions database. BMC Syst Biol. 2017;11(1):50doi: 10.1186/s12918-017-0426-0.
Labena, A. A., Ye, Y. N., Dong, C., Zhang, F. Z., & Guo, F. B. (2017). SSER: Species specific essential reactions database. BMC systems biology, 11(1), 50. https://doi.org/10.1186/s12918-017-0426-0
Labena, Abraham A, et al. "SSER: Species specific essential reactions database." BMC systems biology vol. 11,1 (2017): 50. doi: https://doi.org/10.1186/s12918-017-0426-0
Labena AA, Ye YN, Dong C, Zhang FZ, Guo FB. SSER: Species specific essential reactions database. BMC Syst Biol. 2017 Apr 19;11(1):50. doi: 10.1186/s12918-017-0426-0. PMID: 28420402; PMCID: PMC5395902.
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BMC Syst Biol. 2017 Apr 19;11(1):50. doi: 10.1186/s12918-017-0426-0.

SSER: Species specific essential reactions database.

BMC systems biology

Abraham A Labena, Yuan-Nong Ye, Chuan Dong, Fa-Z Zhang, Feng-Biao Guo

Affiliations

  1. Center of Bioinformatics, Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.
  2. Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.
  3. College of Computational and Natural Sciences, Dilla University, Dilla, Ethiopia.
  4. School of Biology and Engineering, Guizhou Medical University, Guiyang Shi, China.
  5. Center of Bioinformatics, Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China. [email protected].
  6. Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China. [email protected].
  7. Bioinformatics Center in School of Life Science and Technology, University of Electronic Science and Technology of China, No.4, Section 2, North JianShe Road, Chengdu, 610054, China. [email protected].

PMID: 28420402 PMCID: PMC5395902 DOI: 10.1186/s12918-017-0426-0

Abstract

BACKGROUND: Essential reactions are vital components of cellular networks. They are the foundations of synthetic biology and are potential candidate targets for antimetabolic drug design. Especially if a single reaction is catalyzed by multiple enzymes, then inhibiting the reaction would be a better option than targeting the enzymes or the corresponding enzyme-encoding gene. The existing databases such as BRENDA, BiGG, KEGG, Bio-models, Biosilico, and many others offer useful and comprehensive information on biochemical reactions. But none of these databases especially focus on essential reactions. Therefore, building a centralized repository for this class of reactions would be of great value.

DESCRIPTION: Here, we present a species-specific essential reactions database (SSER). The current version comprises essential biochemical and transport reactions of twenty-six organisms which are identified via flux balance analysis (FBA) combined with manual curation on experimentally validated metabolic network models. Quantitative data on the number of essential reactions, number of the essential reactions associated with their respective enzyme-encoding genes and shared essential reactions across organisms are the main contents of the database.

CONCLUSION: SSER would be a prime source to obtain essential reactions data and related gene and metabolite information and it can significantly facilitate the metabolic network models reconstruction and analysis, and drug target discovery studies. Users can browse, search, compare and download the essential reactions of organisms of their interest through the website http://cefg.uestc.edu.cn/sser .

Keywords: Database; Essential Reactions; Flux Balance Analysis (FBA); Metabolic Networks; SSER

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