[gmx-users] Docking

[mohsen ramezanpour]

Dear Aldo

Thank you for your reply
Mark's notes and yours were very useful.

Best
mohsen

On Wed, Apr 27, 2011 at 6:46 PM, Aldo Segura <asegurac666 at yahoo.com.mx>wrote:

> Before making a MD simulation you should try to explore different ways to
> analyze your docking results. For example, performing the same experiment
> with different docking programs and scoring functions (“consensus scoring”)
> and compare the results, is there consistency between them?. Now, if docking
> results are not successful in terms of prior knowledge of your system (is
> there structural information of your system? articles?), you could select
> several of the complex predicted by the docking program and make a MD
> simulation and free energy calculation, compare the results for each complex
> and verify if the results improve according to what you expected. However,
> as mentioned by Mark, simulations and calculations like these involve much
> computational resources and time.
>
>
>
> Best regards,
>
>
> Aldo
>
> **
>
> *=======================================
> Aldo Segura-Cabrera
> Laboratorio de Bioinformática
> Centro de Biotecnología Genómica
> Instituto Politécnico Nacional
> Blvd. Del Maestro esquina Elías Piña, 88710
> Reynosa, Tamaulipas, México.
> (899)9243627 ext. 87747
> e-mail: asegurac at ipn.mx; aldosegura at gmail.com
> =========================================*
>
>
> --- El *mié 27-abr-11, Mark Abraham <Mark.Abraham at anu.edu.au>* escribió:
>
>
> De: Mark Abraham <Mark.Abraham at anu.edu.au>
> Asunto: Re: [gmx-users] Docking
> A: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Fecha: miércoles, 27 de abril de 2011, 5:27
>
> On 4/27/2011 7:52 PM, mohsen ramezanpour wrote:
>
> Dear Mark
> Thank you for your reply.yes,you are right.
>
> Regarding question 2:
> I have a pdf file from "Docking Server" for sertraline-SERT example.Suppose
> this is a good docked state.
>
> In the other hand,I did what I explained in section 1 for sertraline and
> SERT.(by pymol and ...)
> Now, I want to check if I have docked sertraline to SERT correctly or not(
> by comparing with Docking server's one)
> How can I do that?
>
>
> Comparing MD-docked structures and otherwise-docked structures is easy -
> look at the RMS deviation of atom positions, to start with. However, a small
> or large deviation is not evidence that either docked structure bears any
> relationship to what happens in vivo.
>
>
> Do you have any suggestion for doing docking by gromacs? for example
> pulling code, MD , or SMD?
>
>
> People use these kinds of methods for good reasons. Time spent reading up
> on how and why is time well spent.
>
> Mark
>
>  Thanks in advance
>
>
> On Wed, Apr 27, 2011 at 1:48 PM, Mark Abraham <Mark.Abraham at anu.edu.au<http://mc/compose?to=Mark.Abraham@anu.edu.au>
> > wrote:
>
> On 4/27/2011 7:05 PM, mohsen ramezanpour wrote:
>
> Dear Users
>
> I read so many emails to mailing list, there were important notes about
> docking but I couldn't extract a general result.
> Please let me know:
>
> 1-Can we dock a ligand to it's protein's binding pocket with Pymol and
> Gromacs as following?
>
> first:locating ligand outside and close to binding site  manually in pymol
> and saving complex.pdb
> second:doing all steps for generating complex.top and complex.gro as
> Enzyme-Drug tutorial
> third:running md (with out any pull code and constraint),in the other
> words,full flexible system.
>
> I think drug can move freely and according to it's interaction with binding
> site can be attracted by binding site.
> reside for a distance time and then will come out of pocket.
>
> Am I right?
>
>
>  In principle, yes, but it is wildly unlikely that you have a system that
> can bind and unbind reliably in the 100ns simulation range that you might be
> able to afford to run, and if you did happen to have one, what would you
> have learned?
>
>
>  I know what discussed in mainling list about deffinition of "Docking".
>
>
> 2-I have some docked files by "Docking Server " for some of my
> drug-protein's complexes.
> now,I want to obtain them by doing MD in the above proccess.if I was
> successful then try to do that for other drugs which I don't have any docked
> pdb for them.
>
> How can I fit a trajectory with a typical pdb file?
>
>
>  I don't understand what you are asking.
>
> Mark
>
>
>
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