CCL: docking programs, which account for T-shaped pi-pi interactions



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" <owner-chemistry(~)ccl.net> wrote:


Sent to CCL by: Andrew Voronkov [drugdesign[A]yandex.ru]
Dear CCL users, we have published a model with docked ligand. The X-ray, which was done after publication shows that it was wrong.
As I understand the cause for error was that in ligand-protein interactions the T-shaped stacking between ligand's aromatic ring and aromatic ring of Phe 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, which can account for this type of interactions.
Basically those, which can accurately reproduce different types of interactions, including this type and different types of pi interactions.
That is probably quite general problem for docking. But I am just curious if docking methods can accurately account for such interactions, or that should be some quantum, mechanics methods or maybe this program from Shroedinger group http://www.schrodinger.com/productpage/14/18/? Has anyone been working with this type of interactions?

Best regards,
Andrew
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