Retrosynthetic analysis - Revision history

Frodo: /* run program */ asdf

2016-01-20T19:35:23Z

run program: asdf

← Older revision		Revision as of 19:35, 20 January 2016
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	== run program ==		== run program ==
	zinc-manage -e shell retrosynth --smiles="Cc3ccn2nc(CCCC(=O)Nc1ccc(O)cc1C)cc2c3" --recursions=0 --show=successful		zinc-manage -e shell utils retrosynth analyze --smiles="Cc3ccn2nc(CCCC(=O)Nc1ccc(O)cc1C)cc2c3" --recursions=0 --show=successful

	=== sample output and explanation ===		=== sample output and explanation ===

Teague Sterling: /* run program */

2016-01-07T18:22:54Z

run program

← Older revision		Revision as of 18:22, 7 January 2016
Line 6:		Line 6:
	== run program ==		== run program ==
	zinc-manage -e shell retrosynth --smiles="Cc3ccn2nc(CCCC(=O)Nc1ccc(O)cc1C)cc2c3" --recursions=0 --show=successful		zinc-manage -e shell retrosynth --smiles="Cc3ccn2nc(CCCC(=O)Nc1ccc(O)cc1C)cc2c3" --recursions=0 --show=successful

	== sample output and explanation		=== sample output and explanation ===
	<pre>		<pre>
	Line-1 (1 options)		Line-1 (1 options)

Teague Sterling: /* run program */

2016-01-07T18:22:16Z

run program

← Older revision		Revision as of 18:22, 7 January 2016
Line 5:		Line 5:

	== run program ==		== run program ==
	~~zinc_manage~~ retrosynth --smiles="Cc3ccn2nc(CCCC(=O)Nc1ccc(O)cc1C)cc2c3" --recursions=0 --show=successful		zinc-manage -e shell retrosynth --smiles="Cc3ccn2nc(CCCC(=O)Nc1ccc(O)cc1C)cc2c3" --recursions=0 --show=successful

	== sample output and explanation		== sample output and explanation

Teague Sterling: /* set up environment */

2016-01-07T18:21:50Z

set up environment

← Older revision		Revision as of 18:21, 7 January 2016
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	source /nfs/soft/dock/DOCK37/env.csh		source /nfs/soft/dock/DOCK37/env.csh
	source /nfs/soft/www/apps/zinc15/envs/internal/env.csh		source /nfs/soft/www/apps/zinc15/envs/internal/env.csh
	~~setenv ZINC_CONFIG_ENV shell~~

	== run program ==		== run program ==

Frodo: asdf

2015-10-28T23:10:50Z

asdf

New page

== set up environment ==

source /nfs/soft/dock/DOCK37/env.csh
source /nfs/soft/www/apps/zinc15/envs/internal/env.csh
setenv ZINC_CONFIG_ENV shell

== run program ==
zinc_manage retrosynth --smiles="Cc3ccn2nc(CCCC(=O)Nc1ccc(O)cc1C)cc2c3" --recursions=0 --show=successful

== sample output and explanation
<pre>
Line-1 (1 options)
Successful Synthesis via negishi coupling in 1 steps
Cc1ccn2nc(CCl)cc2c1 . Cc1cc(O)ccc1NC(=O)CCCl >> Cc1ccn2nc(CCCC(=O)Nc3ccc(O)cc3C)cc2c1
Reactant 1: Cc1ccn2nc(CCl)cc2c1 - Purchasable as ZINC000238540793
Reactant 2: Cc1cc(O)ccc1NC(=O)CCCl - Purchasable as ZINC000041725839
</pre>

If you want a bit more diversity you could change --show to partial to get reactions where less than all (but more than none) of the reactants were available. This also may be useful if you want to use a different reaction. You can the either run similarity searches around the unresolved reactants or try to increase the --recursions to try a few more steps... That can get out of hand above 2 or 3 though (not that you'd want to do that).

== step 2 - Gets ZINC IDS ==
* 1) ZINC000238540793
* 2) ZINC000041725839

I then ran a similarity search for building block compounds containing the reactive group for the left and right side of a Negishi coupling (no easy interface available for this yet)

These are left.smi and right.sim in /nfs/work/teague/MK/

These current results are at 70% Tanimoto because I misplaced the 50% Tanimoto downloads (doh!)

== step 3 ==
I then ran the reactor in DOCK37 ($DOCKBASE/ligand/reactor/react.py) with the RXN SMARTS for the Negishi coupling ( "[#6:1]-,:[#17,#35,#53].[#6:2]-[#17,#35,#53]>>[#6:1]-[#6:2]" )
and the left.smi and right.smi and filtered for duplicates. This creates synthetic.smi. Modify that to be better suited for db2 generation.

(all in the run.sh script in that directory).

== step 4 ==

Run database building using the DOCK37 pipeline.

$DOCKBASE/ligand/generate/build_smiles_ligand.sh database.smi

For the new compound you showed me, I think we need to investigate the reactions and see which one is failing to validate.

I am building the db2 files now in that directory.

[[Category:Tutorials]]
[[Category:Synthesis]]
[[Category:Organic chemistry]]
[[Category:Reactions]]