Re: : PAINS filtering

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

Re: : PAINS filtering

Chris Swain
If you are planning to annotate very large data sets it might be worth looking at Vortex.

http://macinchem.org/reviews/vortex/tut24/scripting_vortex24.php

Pains matching PubChem 67M structures took under 4 hours.

Chris


>
> Message: 6
> Date: Tue, 15 Mar 2016 10:54:11 -0700
> From: Stefano Forli <[hidden email]>
> Subject: Re: [Open Babel] PAINS filtering
> To: mirix <[hidden email]>,
> "[hidden email]"
> <[hidden email]>
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset="windows-1252"; format=flowed
>
> About that, a while ago I had compiled an OB-compatible data file with the three pattern
> classes (L15, L150 and M150) from Raj Gua [1].
>
> Dirt cheap implementation with Pybel works fine, but the main issue is timing. Processing
> a Mol2 file with 1000 random molecules from the ZINC database takes about 13 seconds.
> Not bad, but not even fast: to process a pretty large library for virtual screning  (e.g,
> ChemBridge library, 1.5M compounds) would take about 5.4 hours.
>
> I'm not sure if there's a way to speed up the process, but if so, it should be definitely
> considered.
>
> Anyway, let me know what would be the best way to share the files, and I'll do it.
>
> Cheers,
>
> S
>
>
> [1] http://blog.rguha.net/?p=850
>


------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss