CCL: in silico biotargets fishing - reverse screening
- From: Andreas Bender <bender.andreas%a%gmail.com>
- Subject: CCL: in silico biotargets fishing - reverse screening
- Date: Sun, 16 Jan 2011 09:21:59 +0000
Sent to CCL by: Andreas Bender [bender.andreas+*+gmail.com]
Hi Andrew,
There are several methods around to predict protein targets of small
molecules, both ligand-based and structure-based ones.
One example of the ligand-based approaches is SEA from the Shoichet
group (http://sea.bkslab.org/) which is based on fingerprints. Last
year also a webtool, PharmMapper, has been published which allows you
to predict targets using pharmacophores, the address is
http://59.78.96.61/pharmmapper/. So there are the web
interfaces, but
on the other hand it's also relatively easy to take all the
bioactivity data from e.g. ChEMBL and train a multi-class model on
fingerprints or any other descriptors you find relevant.
A recent review article on the topic has been written by Ma et al.,
http://www.ncbi.nlm.nih.gov/pubmed/20221898. We also wrote
one in 2007
which you can find here:
http://dx.doi.org/10.1016/j.ddtec.2006.12.008. Currently I
am
finishing another review article on the topic, so if you (or anyone
else on the list) is interested in receiving a copy when published
please just let me know.
Best wishes,
Andreas
--
Andreas Bender, PhD
Lecturer for Molecular Informatics
Unilever Centre, Cambridge University
http://www-ucc.ch.cam.ac.uk
Personal: http://www.andreasbender.de
On Fri, Jan 14, 2011 at 11:24 AM, Andrew Voronkov
drugdesign[]yandex.ru <owner-chemistry-#-ccl.net> wrote:
>
> Sent to CCL by: Andrew Voronkov [drugdesign+*+yandex.ru]
> Dear CCL users,
> I have seen a very interesting presentation from Intelligand on biotargets
in silico deconvolution for the known compounds. This is pharmacophore-based
screening approach for some sets of biotargets. What are other methods, software
and approaches available for in silico biotarget identification for compounds
without know targets-mechanisms of action? The best of course would be to find
some tools which is possible to use locally?
>
>
> Best regards,
> Andrew> http://www.ccl.net/cgi-bin/ccl/send_ccl_message>
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