Chemical reactions: Difference between revisions

Latest revision as of 04:21, 1 October 2015

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.

new JSME has some support for reaction smarts, although frankly, hey, I appreciate they are trying, but I still code them by hand.
[http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html Daylight[
RDKit
chemaxon

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

@@ Line 21: / Line 21: @@
 * new JSME has some support for reaction smarts, although frankly, hey, I appreciate they are trying, but I still code them by hand.
 *  [http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html Daylight[
-* [http://www.rdkit.org/docs/RDKit_Book.html rdkit]
+* [http://www.rdkit.org/docs/RDKit_Book.html RDKit]
 * [https://docs.chemaxon.com/display/reactor/User's+Guide chemaxon]
-nb there are subtle and not to subtle differences between versions. We use rdkit.
+nb there are subtle and not to subtle differences between versions. We use [[RDKit]].
 [[Category:Tutorial]]
 [[Category:ZINC15]]