Reactant pairs and reaction organization patterns produced by a new rule-based approach

BMC Research Notes
Carlos Vazquez-HernandezRosa-Maria Gutierrez-Rios

Abstract

Improvements in bioinformatics applications for the enzyme identification of biochemical reactions, enzyme classifications, mining for specific inhibitors and pathfinding require the accurate computational detection of reaction similarity. We provide a set of substrate-product pairs, clustered by reactions that share similar chemical transformation patterns, for which accuracy was calculated, comparing this set with manually curated data sets. The data were analyzed by a new method that naturally split each reaction into compound pairs and loner compounds, which we called architectures (Vazquez-Hernandez et al. in BMC Syst Biol 12:63, 2018). The data include a set of 7491 curated reactions from the KEGG-Ligand data set. The data are presented in two formats, a string format and a tree structure, both of which reflect the splitting process and the final architectures of each reaction. We are also reporting sets of reactions that show similar splitting patterns naturally grouped into clusters of tree structures. The compound pairs in each cluster were compared with the reactant pairs proposed by the KEGG-RCLASS data set, and a match precision value is also provided. These data were collected with the aim of providing research wit...Continue Reading

References

Dec 26, 2001·Nucleic Acids Research·Minoru KanehisaAkihiro Nakaya
Mar 14, 2009·Journal of Molecular Biology·Karoline FaustJacques van Helden
Sep 12, 2012·Journal of Chemical Information and Modeling·Mario LatendressePeter D Karp
Nov 1, 2017·Journal of Cheminformatics·German A Preciat GonzalezRonan M T Fleming
Mar 20, 2018·Synthetic and Systems Biotechnology·Lin WangCostas D Maranas
Jun 1, 2018·BMC Systems Biology·Carlos Vazquez-HernandezRosa-Maria Gutierrez-Rios

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Citations

Jul 1, 2020·American Journal of Physiology. Gastrointestinal and Liver Physiology·Xi QianCheleste M Thorpe

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Software Mentioned

RCLASS
Perl scripts
RPAIR

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