Chemical reactions

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People write us asking about doing chemical reactions in the computer to create new libraries of compounds.

Using DOCK (github) use:

source /nfs/soft/python/envs/complete/latest/env.csh
cd ~/code/DOCK/ligand/reactor/
./reactsmi.py --serve

then go to

gimel.compbio.ucsf.edu:8081
  • step 1. enter reaction smarts
  • step 2. choose file containing reactant 1, one per line, smiles followed by identifier
  • step 3. choose file reactant 2, one per line, smiles followed by identifier
  • click on react
  • step 4. profit

NB this will be a public service soon.

It has not escaped the attention of the authors that writing reaction smarts is a bfd. Fortunately, there are many resources that can help.

nb there are subtle and not to subtle differences between versions. We use RDKit.