[Zinc-fans] SEA predictions

John J. Irwin jji at cgl.ucsf.edu
Mon May 4 13:35:26 PDT 2009


Hi Menachem

Thanks for your interest in ZINC and SEA.

Menachem Shoham wrote:
> Hi,
>
> My questions are about SEA predictions:
>
> 1. What does SEA stand for?
Similarity Ensemble Approach. See http://sea.docking.org/ for the Nat
Biotech paper reference and the website implementation.
>
> 2. What does pPvalue:10 mean?
The p is as in -log10, so the P-value is 10^-10.  This can be read as
"you would expect to draw 10^10 molecules at random to find out that was
as similar to the annotated compounds as this one is".  Our cutoff for
"interesting" SEA predictions is often 10^-10.  Whereas this does not
guarantee the ligand will be active, it is worth looking at.
>
> 3. What does maxTC:44 mean?
Maximum Tanimoto Coefficient.  The nearest neighbor of this ligand to
the annotated ligands for this annotation is 44%. 100% would mean it was
identical to an annotated ligand, and thus uninteresting.  The
fingerprint used is a daylight-mimic, so 44% is unrecognizably different.
>
> 4. How do I retrieve the original information about this biological
> activity?
>     Clicking on this particular line just gets me a list of all
> compounds with this activity.
We use Wombat and MDDR, both of which cost money. If you have a Wombat
or MDDR license, we can give you click through access to see the source
database compounds. You can fax it through to 415-514-4260 attn John
Irwin. 

When Starlite becomes available, we will make Starlite compounds visible
directly, since this database will be free.

I hope this helps!

John
Joint member, UCSF ZINC Team and UCSF SEA Team

>
> Thanks,
> Menachem Shoham
>
> Menachem Shoham, Ph.D.
>
> Case Western Reserve University
>
> School of Medicine, Department of Biochemistry
>
> 10900 Euclid Ave
>
> Cleveland, OH 44106-4935
>
> Tel. 216-368-4665
>
> Fax  216-368-3419
>
> E-mail: mxs10 at case.edu <mailto:mxs10 at case.edu>
>
> http://www.cwru.edu/med/biochemistry/faculty/shoham.html
>
>
>
>
>
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>
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