RxnPattern (FAQ)
Q: What can I GET from RxnPattern?
A: You can get 990 chemical transformation patterns generalized from 4382 biochemical reactions.
Q: What is the RxnPattern's purpose?
A: A mapping is built between the patterns and EC numbers (up to sub-sub classes), which provides an intuitive method to map biochemical space. The patterns could be used as "fabrication core catalyzed" in information-guided pathway design.
Q: What is a reaction pattern?
A: Reaction pattern is a combination of molecular fragments composed of reaction centers (bonds changed during a reaction).
Q: How to curate reaction pattern?
A: (The first step:) Get atom alignments for a biochemical reaction. For example, atom alignments of RPAIR database from KEGG database. Atom mapping of BioPath from Gasteiger's group. You can also map the atoms using your expert knowledge.
(The second Step:) Identify bonds (reaction centers) changed during a reaction. Reaction centers refer to those chemical bonds formed or broken during a reaction process.
(The third Step:) Link those bonds into a fragment for each molecule.
(The fourth Step:) Combine these fragments into a smirks string (examples are available from JCIM 1999, 39(6), 1161-1172).
Q: Reaction pattern Examples?
A: (Oxidoreductases:) CO.c1cccnc1>>C=O.N1C=CCC=C1 for R08306 et al..
(Transferases:) CS.O>>CO.S for R07330 et al..
(Hydrolases:) NC=O.O>>N.OC=O for R03909 et al..
(Lyases:) OCCO>>CC=O.O for R01209 et al.
(Isomerases:) O.C=CC=O>>OCCC=O for R07795 et al..
(Ligases:) OC=O.OPOP.S>>O.OP.SC=O for R01280 et al..
Q: Statistics on reaction patterns?
A: Currently, there are 990 reaction patterns extracted from 4382 KEGG reactions.
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