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connorcoley / rdchiral

Wrapper for RDKit's RunReactants to improve stereochemistry handling
MIT License
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Special Functional Group List in Biochemical reactions #46

Open 0m1n0 opened 11 months ago

0m1n0 commented 11 months ago

Dear @connorcoley,

Your team's paper on Merging enzymatic and synthetic chemistry with computational synthesis planning is absolutely excellent! As I'm not an expert in chemoinformatics, your work helps people like me: I understand your ideas but I could never implement them so explicitly...!

I'm especially interested how you apply RDChiral on BKMS database in order to get reaction templates. Today I'm trying to:

  1. Reproduce data processing of BKMS following Jupyter Notebooks https://github.com/itai-levin/hybmind/tree/main/process_BKMS_database/Notebooks (almost done)
  2. Apply the same data processing steps to MetaCyc and Rhea databases (I'm currently working on these data bases)
  3. Apply RDChiral on 2

In RDChiral, you set "Special functional groups" (Table S1 of the paper, and in template_extractor.py of RDChiral). Did you use the same list for BKMS or did you customise it for biochemical reactions? If so, how did you create this list?

Kind regards, Min