How are RDM patterns for reactions in the KEGG database constructed? [closed]








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With respect <http://www.genome.jp/dbget-bin/www_bget?rp:RP00167>   
  

can anyone tell me how the RDM pattern were obtained??   
  
 Information what RDM is given here:   
  
<http://www.genome.jp/kegg/reaction/>   
  

  
  
Note: This may be a silly question to all chemists, but not for me, i am a computer science student , and my research field in bioinformatics and so i have to study both biology and bit of chemistry, so please just dont close the question or be harsh on me, I have very little knowledge in chemistry and also googling doesn't help much. I asked this question in Biology forum, they closed the question and asked me to ask it here




To my impression, there is no RDM **value**, but a RDM **pattern**!


This is about mapping atoms is a reactant and a product by assigning **R** (*reaction center*), **D** (*difference atoms*) and **M** (*matched atoms*) in both compounds. Pairs for **R**, **D**, and **M** are separated by colons. The pattern is thus given as 


**R**(reactant)-**R**(product) : **D**(reactant)-**D**(product) : **M**(reactant)-**M**(product), 


where a an asterisk marks a void centre.


In order to figure out how these patterns are retrieved, you definitely want to have a look at *Modular Architecture of Metabolic Pathways Revealed by Conserved Sequences of Reactions*, a freely available article by *Minoru Kanehisa* (KEGG founder), published in *J. Chem. Inf. Model.*, **2013**, *53*,613-622 ([DOI](http://dx.doi.org/10.1021/ci3005379)). Don't forget to read the [Supporting Information](http://pubs.acs.org/doi/suppl/10.1021/ci3005379/suppl_file/ci3005379_si_001.pdf), particularly the sections on **KEGG atom types** and **RDM chemical transformation notation**.


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