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2024-05-02T17:26:48Z

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← Older revision		Revision as of 17:26, 2 May 2024
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	-- John		-- John

			[[Category:Aggregators]]
			[[Category:API]]
			[[Category:Update needed]]

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2016-12-15T21:18:22Z

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← Older revision		Revision as of 21:18, 15 December 2016
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	There is a way to script this. It is similar to but not exactly the same as the aggregator advisor.		There is a way to script this. It is similar to but not exactly the same as the aggregator advisor.
	If you want the scripted version, please write me.		If you want the scripted version, please write me.

			curl http://zincfifteen.docking.org/patterns/apps/checker.txt -F upload=@smiles_file -F pains=y -F aggregators=y

			please do not over use this feature. Slow! works best with < 100 smiles per transactions

	-- John		-- John

Frodo: asdf

2016-04-19T18:05:22Z

asdf

New page

To script testing for aggregators, you have two options, aggregator advisor and ZINC15.

= Aggregator advisor =
* Download the python script simi.py which may be found at http://advisor.bkslab.org/faq/#Command.
Prepare your molecules to be tested. Here we test the first 100 FDA approved compounds from ZINC
wget zinc15.docking.org/substances/subsets/fda.smi
The file looks like this
$ grep -n ZINC000000020237 fda.smi
32:CCN(CC)CC(=O)Nc1c(C)cccc1C ZINC000000020237
* Run the program as
python simi.py similar fda.smi > output
* When there are matches to aggregators, each line contains :
** original smiles
** matched aggregator
** tanimoto similarity (in the paper we suggest 0.85 cutoff, but we are more generous in the calculation here to allow you to make the cut
** original identifier from the input file
* e.g. the first line of output is as follows
$ python simi.py similar fda.smi
CCN(CC)CC(=O)Nc1c(C)cccc1C Cc1cccc(C)c1NC(=O)CNc1ccccc1 0.87 ZINC000000020237

= ZINC15 =
We now have a bulk processing facility, the right hand side of
http://zinc15.docking.org/patterns/home/.
It supports both PAINS and Aggregator similarity searches.

To use it, paste SMILES, one per line, or upload a file,
up to 1000 per transaction. A whitespace-separated identifier after
the SMILES is optional. It can be used with curl programmatically if
you prefer.

For instance, if you enter:
CCOc1ccc([C@@H]2[C@H]3CCCC=C3C(C#N)=C(N)C2(C#N)C#N)cc1 some_identifier

and click on "Check" you will see it matches: cyano_ene_amine_A(56)

If you enter:
C1=CC(=C(C=C1C2=C(C(=O)C3=C(C=C(C=C3O2)O)O)O)O)OC blah_blah_blah

and click on "Check" you will see it is similar to an aggregator, and
we have a button that allows you to run it again in the Aggregator
Advisor as published recently in J Med Chem. We've used ECFP4 Tc 0.6
instead of axonpath 0.85 as in the paper, so it is an approximation.
0.55 ECPF4 might be better, we're still testing.

There is a way to script this. It is similar to but not exactly the same as the aggregator advisor.
If you want the scripted version, please write me.

-- John

Scripted testing for aggregators - Revision history

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