[gmx-users] Re: Re:rather theoretical question

Dmitry Egorov egorov at newhospital.ru
Fri Jul 4 05:13:01 CEST 2003

Dear Alexander Yakovenko, thank you very much for your answer, I just wanted
know how much are the chances that MD can  right fit ligand from one X-ray
protein-ligand conformation to another, theoretical derived from first apo
structure ( not with MD) conformation, where ligand state is not known. So
as I understood, it is likely not possible to obtain  with good probability
wanted structure. Once more  thank you very much.
D. Egorov.
----- Original Message -----
From: alexander yakovenko <yakovenko_a at ukr.net>
To: <egorov at newhospital.ru>
Cc: <gmx-users at gromacs.org>
Sent: Thursday, July 03, 2003 5:05 PM
Subject: Re:rather theoretical question

> Dear D. Egorov
> If C1 and C2 is a X-ray structures it is not possiable to reproduce
structures (I
> have never found it). But you may found position, when the dynamics
> simulations are similar. Calculate near 1.2ns of dynamic for both
> link trajectories into one file,  make  index group of your ligand and
> sites residues and make clustering for this group to linked trajectory.
You can
> found some clusteres, which contain frames from trajectory 1 and
trajectory 2
> (time less 1.2 ns and time more 1.2 ns) in one cluster. This work at my
> of near 300 residues.
> 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 Gromacs users, could anybody answer next question.
> >
> >Suppose, we have two different conformations of the same enzyme-cofactor
> >complex,say, C1 and C2. Further, conformations of ligand binding sites
> >and ligands themselves are also different for these C1 and C2 states.
> >Then we place,say, ligand in conformation from C2 to binding site of C1
> >( with previously deleted C1 ligand ). How is it reasonable  to wait
> >that MD convert C2 ligand conformation to right for receptor C1 state
> >and reproduce right ligand fit. What complications may occur here.

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