From owner-chemistry ^%at%^ ccl.net Mon Jan 28 10:36:00 2013 From: "Chris Swain swain]-[mac.com" To: CCL Subject: CCL: docking programs, which account for T-shaped pi-pi interactions Message-Id: <-48141-130128093141-9065-yde+LqUW4EARJUR++3r4yg:server.ccl.net> X-Original-From: Chris Swain Content-type: multipart/alternative; boundary="Boundary_(ID_KQ0HBy1tCnRvikhIHOjL5Q)" Date: Mon, 28 Jan 2013 14:31:32 +0000 MIME-version: 1.0 Sent to CCL by: Chris Swain [swain-*-mac.com] --Boundary_(ID_KQ0HBy1tCnRvikhIHOjL5Q) Content-type: text/plain; charset=utf-8 Content-transfer-encoding: quoted-printable Have you tried the Cresset software? http://www.cresset-group.com/ Chris Sent from my iPad On 28 Jan 2013, at 09:31, "Andrew Voronkov drugdesign/./yandex.ru" wrote: >=20 > Sent to CCL by: Andrew Voronkov [drugdesign[A]yandex.ru] > Dear CCL users, we have published a model with docked ligand. The X-ray, w= hich was done after publication shows that it was wrong. > As I understand the cause for error was that in ligand-protein interaction= s the T-shaped stacking between ligand's aromatic ring and aromatic ring of P= he plays an important role. Docking was performed by GoldSuite. > I have analyzed different docking poses and none of them was correct. > I am curious about docking programs or docking poses evaluation methods, w= hich can account for this type of interactions. > Basically those, which can accurately reproduce different types of interac= tions, including this type and different types of pi interactions. > That is probably quite general problem for docking. But I am just curious i= f docking methods can accurately account for such interactions, or that shou= ld be some quantum, mechanics methods or maybe this program from Shroedinger= group http://www.schrodinger.com/productpage/14/18/? Has anyone been workin= g with this type of interactions? >=20 > Best regards, > Andrew > -------- =D0=97=D0=B0=D0=B2=D0=B5=D1=80=D1=88=D0=B5=D0=BD=D0=B8=D0=B5 =D0=BF= =D0=B5=D1=80=D0=B5=D1=81=D1=8B=D0=BB=D0=B0=D0=B5=D0=BC=D0=BE=D0=B3=D0=BE =D1= =81=D0=BE=D0=BE=D0=B1=D1=89=D0=B5=D0=BD=D0=B8=D1=8F -------- >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script =3D= ->=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20>=20>=20>=20>=20 >=20 --Boundary_(ID_KQ0HBy1tCnRvikhIHOjL5Q) Content-type: text/html; charset=utf-8 Content-transfer-encoding: quoted-printable
Have you tried the Cresset software?

http://www.cresset-group.com/

Chris

Sent f= rom my iPad

= On 28 Jan 2013, at 09:31, "Andrew Voronkov drugdesign/./yandex.ru" <owner= -chemistry(~)ccl.net> wrote:


Sent to C= CL by: Andrew Voronkov [drugdesign[A]yandex.ru<= /a>]
Dear CCL users, we have published a model with docked l= igand. The X-ray, which was done after publication shows that it was wrong.<= /span>
As I understand the cause for error was that in ligand-prote= in interactions the T-shaped stacking between ligand's aromatic ring and aro= matic ring of Phe plays an important role. Docking was performed by GoldSuit= e.
I have analyzed different docking poses and none of them w= as correct.
I am curious about docking programs or docking p= oses evaluation methods, which can account for this type of interactions.
Basically those, which can accurately reproduce different type= s of interactions, including this type and different types of pi interaction= s.
That is probably quite general problem for docking. But I= am just curious if docking methods can accurately account for such interact= ions, or that should be some quantum, mechanics methods or maybe this progra= m from Shroedinger group http://www.schrodinger.com/productpage/14/18/? Has anyone been w= orking with this type of interactions?

Best= regards,
Andrew
-------- =D0=97=D0=B0=D0=B2= =D0=B5=D1=80=D1=88=D0=B5=D0=BD=D0=B8=D0=B5 =D0=BF=D0=B5=D1=80=D0=B5=D1=81=D1= =8B=D0=BB=D0=B0=D0=B5=D0=BC=D0=BE=D0=B3=D0=BE =D1=81=D0=BE=D0=BE=D0=B1=D1=89= =D0=B5=D0=BD=D0=B8=D1=8F --------


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