From owner-chemistry \\at// ccl.net Sun Jan 16 08:57:00 2011 From: "nathanael weill naweill-*-gmail.com" To: CCL Subject: CCL: in silico biotargets fishing - reverse screening Message-Id: <-43657-110116001317-31352-HEchTXI1ow5fq8yfLINZtQ*|*server.ccl.net> X-Original-From: nathanael weill Content-Type: multipart/alternative; boundary=0016363b84b0a9ffec0499efb86a Date: Sun, 16 Jan 2011 00:13:01 -0500 MIME-Version: 1.0 Sent to CCL by: nathanael weill [naweill^gmail.com] --0016363b84b0a9ffec0499efb86a Content-Type: text/plain; charset=ISO-8859-1 Hi, many approaches exists and can be classified in 3 groups: 1) Protein based. By comparing proteins, known binders from protein A can be predicted as binder of protein B if protein A and protein B are very similar. 2) ligand based. By comparing ligands, if a molecule is similar to a known binder of a protein, then the molecule can be exected to bind this protein. 3) protein ligand based. By comparing complexes of protein ligands, target fishing is possible. In adittion, inverse docking is also possible. I strongly recommend a recent review on that specific topic : http://onlinelibrary.wiley.com/doi/10.1002/minf.200900081/abstract best regards nathanael weill On Fri, Jan 14, 2011 at 6:24 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> > > -- Nathanael WEILL, PhD McGill University Department of Chemistry Otto Maass Building 801 Sherbrooke St. West, lab 206A Montreal, QC, Canada H3A 2K6 Phone: 514-398-5501 Fax: 514-398-3797 nathanael.weill^-^mail.mcgill.ca --0016363b84b0a9ffec0499efb86a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi,
many approaches exists and can be classified in 3 groups:
1) Protein based. By comparing proteins, known binders from protein A= can be predicted as binder of protein B if protein A and protein B are ver= y similar.=A0
2) ligand based. By comparing ligands, if a molecule is similar to a k= nown binder of a protein, then the molecule can be exected to bind this pro= tein.
3) protein ligand based. By comparing complexes of protein = ligands, target fishing is possible.=A0In adittion, inverse docking is also= possible.

I strongly recommend a recent review on that specific t= opic :=A0http://onlinelibrary.wiley.com/doi/10.1002/m= inf.200900081/abstract

best regards
nathanael weill

On Fri, Jan 14, 2011 at 6:24 AM, Andrew Voronkov drugde= sign[]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-base= d screening approach for some sets of biotargets. What are other methods, s= oftware and approaches available for in silico biotarget identification for= compounds without know targets-mechanisms of action? The best of course wo= uld be to find some tools which is possible to use locally?


Best regards,
Andrew



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--
=A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0
Nathanael WEILL, PhD
McGill University
Department of Che= mistry
Otto Maass Building
801 Sherbrooke St. West, lab 206A
Montr= eal, QC, Canada
H3A 2K6

Phone: 514-398-5501
Fax: 514-398-3797
nathanael.weill^-^mail.mc= gill.ca

--0016363b84b0a9ffec0499efb86a--