[gmx-users] Docking

[Aldo Segura]

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>
        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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