[gmx-users] Re:rather theoretical question

Dmitry Egorov egorov at newhospital.ru
Tue Jul 8 04:59:01 CEST 2003

Dear Alexander Yakovenko, great thanks for your answers on my questions.
Your and Vojtech Spiwoks's comments are the better, than that I expected to
receive. It's good starting point for me.
Best wishes,
D. Egorov, 08.07.2003.

----- Original Message -----
From: Alexander <yakovenko_a at ukr.net>
To: <egorov at newhospital.ru>
Cc: <gmx-users at gromacs.org>
Sent: Friday, July 04, 2003 8:10 PM
Subject: [gmx-users] Re:rather theoretical question

> Hi Dmitry,
> My experience based on dynamic study of kinase-inhibitor complexes, so
> it will be some differences with native substrates and other
> proteins. The main problem is to find correct energy minima, when
> structures are dynamic. The MD very often reproduces domains moving,
> but they not very sensitive to ligand structure, much more for its
> presence :(, especially in long MD experiments.
> Similar to X-ray structures I had found only with 20-25%
> methanol-water mixes (with GROMOS96FF). If you sure that you apo-
structure correct, you
> can make constrains and so on as say Vojtech Spiwok, but I recommend
> you to use molecular docking with energy minimization and visual
> checking of obtained complexes.
> Best regards,
> Alexander Yakovenko
> Institute of Molecular Biology & Genetic of NAS of Ukraine
> 03143
> acad.Zabolotnogo str. 150
> Kiev
> Ukraine
> ______________________________________________
> E-mail: yakovenko_a at ukr.net
> >Dear Alexander Yakovenko, thank you very much for your answer, I just
> >know how much are the chances that MD can  right fit ligand from one
> >protein-ligand conformation to another, theoretical derived from first
> >structure ( not with MD) conformation, where ligand state is not known.
> >as I understood, it is likely not possible to obtain  with good
> >wanted structure. Once more  thank you very much.
> >D. Egorov.
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