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Reaction Decoder Tool (RDT): extracting features from chemical reactions.

Rahman SA, Torrance G, Baldacci L, Martínez Cuesta S, Fenninger F, Gopal N, Choudhary S, May JW, Holliday GL, Steinbeck C, Thornton JM - Bioinformatics (2016)

Bottom Line: Extracting chemical features like Atom-Atom Mapping (AAM), Bond Changes (BCs) and Reaction Centres from biochemical reactions helps us understand the chemical composition of enzymatic reactions.Reaction Decoder is a robust command line tool, which performs this task with high accuracy.This aids in the analysis of metabolic pathways and the ability to perform comparative studies of chemical reactions based on these features.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Congenica Ltd, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

No MeSH data available.


(a) AAM performed by RDT and the resulting BCs (i.e. formed/cleaved: C%C (Ring), Order Change: C%C*C = C, C-C*C = C) and (b) reaction centres are highlighted in pink colour in the image, where as neighbouring atoms are highlighted in green
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btw096-F1: (a) AAM performed by RDT and the resulting BCs (i.e. formed/cleaved: C%C (Ring), Order Change: C%C*C = C, C-C*C = C) and (b) reaction centres are highlighted in pink colour in the image, where as neighbouring atoms are highlighted in green

Mentions: BCs in chemical reactions refers to the cleavage and formation of chemical bonds, changes in bond order and stereo changes, which are due to chemical processes such as chiral inversions or cis-trans isomerization(s). In the chemical reaction diagram and tables atoms are connected by a bond i.e. single ‘–‘, double ‘=’or ring ‘%’ etc. (Fig. 1a), for instance C–C means a single carbon–carbon bond that is cleaved (‘/’) or formed in the reaction (‘‖’). Bond order changes are represented by star ‘*’, e.g. C–C * C = C means a single carbon–carbon bond turning into double carbon-carbon bond or vice versa. Stereo changes are represented as atoms that change their absolute configuration, for instance C(R/S) means a carbon atom that changes from R to S configuration. A reaction centre is the collection of atoms and bonds that are changed during the reaction (Warr, 2014), also known as the local atomic environment around the atoms involved in BCs.Fig. 1


Reaction Decoder Tool (RDT): extracting features from chemical reactions.

Rahman SA, Torrance G, Baldacci L, Martínez Cuesta S, Fenninger F, Gopal N, Choudhary S, May JW, Holliday GL, Steinbeck C, Thornton JM - Bioinformatics (2016)

(a) AAM performed by RDT and the resulting BCs (i.e. formed/cleaved: C%C (Ring), Order Change: C%C*C = C, C-C*C = C) and (b) reaction centres are highlighted in pink colour in the image, where as neighbouring atoms are highlighted in green
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4920114&req=5

btw096-F1: (a) AAM performed by RDT and the resulting BCs (i.e. formed/cleaved: C%C (Ring), Order Change: C%C*C = C, C-C*C = C) and (b) reaction centres are highlighted in pink colour in the image, where as neighbouring atoms are highlighted in green
Mentions: BCs in chemical reactions refers to the cleavage and formation of chemical bonds, changes in bond order and stereo changes, which are due to chemical processes such as chiral inversions or cis-trans isomerization(s). In the chemical reaction diagram and tables atoms are connected by a bond i.e. single ‘–‘, double ‘=’or ring ‘%’ etc. (Fig. 1a), for instance C–C means a single carbon–carbon bond that is cleaved (‘/’) or formed in the reaction (‘‖’). Bond order changes are represented by star ‘*’, e.g. C–C * C = C means a single carbon–carbon bond turning into double carbon-carbon bond or vice versa. Stereo changes are represented as atoms that change their absolute configuration, for instance C(R/S) means a carbon atom that changes from R to S configuration. A reaction centre is the collection of atoms and bonds that are changed during the reaction (Warr, 2014), also known as the local atomic environment around the atoms involved in BCs.Fig. 1

Bottom Line: Extracting chemical features like Atom-Atom Mapping (AAM), Bond Changes (BCs) and Reaction Centres from biochemical reactions helps us understand the chemical composition of enzymatic reactions.Reaction Decoder is a robust command line tool, which performs this task with high accuracy.This aids in the analysis of metabolic pathways and the ability to perform comparative studies of chemical reactions based on these features.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Congenica Ltd, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

No MeSH data available.