Would be interesting to take a set of compounds and look at a correlation
matrix - maybe one can identify a set of "generally" discriminating bits
that can be used for screening ? Probably not but it could be worth a try
... then memory would go down as well as discriminating power up?
Nik
Andrew Dalke <da...@dalkescientific.com>
12.02.2009 14:56
To
RDKit Discuss <rdkit-discuss@lists.sourceforge.net>
cc
Subject
Re: [Rdkit-discuss] Optimizing SSS in the RDKit
On Feb 12, 2009, at 8:46 AM, Greg Landrum wrote:
> I'm either not understanding completely or I disagree. The queries
> were constructed by fragmenting the molecules I searched through, so
> I'd expect lots of substructure hits (and a lower screen-out rate that
> arbitrary queries against arbitrary molecules).
Ahh, of course.
But I don't think fingerprint screen give, say, 0.001% false rates.
I think they are more in line with what you found. But if the bit
distributions were really uncorrelated for molecules where one is
not a substructure of the other, then I would expect extremely
low false positive rates. 2048 bits should give a lot of
discrimination power if the bits weren't correlated.
> That's a good idea to add to the list of things to look into. It's
> also relatively easy to do because it probably just involves
> increasing the minimum path length included in fingerprints (at least
> as a first step).
Again, I don't have experience with that, but it means
that there's less ability to handle unlikely atom types.
Yes, the larger subgraphs will include them. Don't know.
> Looking at MACCS is a good idea. I'll also put that on the list.
Is this list on a wiki? ;)
Andrew
da...@dalkescientific.com
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