doubts on the process of molecular docking

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doubts on the process of molecular docking

DANIHBK
Greetings, I am new and want to use autodock and my doubts are the following:


1. - what so important is for the process to clear water molecules and to add hydrogens?

2. - what so important is the charges of gasteiger?

3.- I read that the most important thing is the active site, my doubt is if this active site is where are the amino acids?, how can i identify the aminoacids in a molecule?.

4.- when we do the simulation of the active site of the protein with the ligand, that is what we measured?, that is to say, we measured the distance between the atoms or measured the energy that is generated?

5.-  finally, what it is measure in a molecular docking simulation? , that interacts of the active site with the ligand and vice versa? , that is what it interests to us to measure of this interaction and how is measured?


Excuseme by the grammar, because I do not speak English, as you can see I am new in this of the molecular docking, and my main doubts about the process were these.

I take leave waiting for its answer.

Kindly:

Daniel Sepúlveda.
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Re: ADL: doubts on the process of molecular docking

Nicolas Sapay
Hello,

Regarding your questions, I recommend you to go to your favorite
university library and read some books about proteins, thermodynamics
and computational chemistry :). The Autodock manual will also provide
you a good list of reference to understand how Autodock is working,
although it requires some basic knowledge of computational chemistry.  

DANIHBK a écrit :
> Greetings, I am new and want to use autodock and my doubts are the following:
>
>
> 1. - what so important is for the process to clear water molecules and to
> add hydrogens?
Water is remove to simplify the system. Hydrogens, actually polar
hydrogens, are added because they are required to model hydrogen bonds.
Non polar hydrogens are generally fused to their heavy atoms for
simplification.
>  
>
> 2. - what so important is the charges of gasteiger?
>  
Partial charges are required to model the electrostatics of your system.
They are several methods to derive them and the Gasteiger one is not
necessarily the best of them.
> 3.- I read that the most important thing is the active site, my doubt is if
> this active site is where are the amino acids?, how can i identify the
> aminoacids in a molecule?.
>  
By definition, amino acids are molecules with an amine and an carboxylic
moiety. They are the basic component of proteins
> 4.- when we do the simulation of the active site of the protein with the
> ligand, that is what we measured?, that is to say, we measured the distance
> between the atoms or measured the energy that is generated?
>  
This is probably dangerous to use something if you don't know what is
its purpose... I would also add that in molecular docking you don't
measure, but estimate. Concretely, you attempt to estimate the energy of
interaction between two compounds (a protein and a small molecule in
general).

Regards,
Nicolas

> 5.-  finally, what it is measure in a molecular docking simulation? , that
> interacts of the active site with the ligand and vice versa? , that is what
> it interests to us to measure of this interaction and how is measured?
>
>
> Excuseme by the grammar, because I do not speak English, as you can see I am
> new in this of the molecular docking, and my main doubts about the process
> were these.
>
> I take leave waiting for its answer.
>
> Kindly:
>
> Daniel Sepúlveda.
>  

________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

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Re: ADL: doubts on the process of molecular docking

DANIHBK
This post has NOT been accepted by the mailing list yet.
I have bioinformatics books, but it does not come specified what I ask, and if you are going to respond trivialities to me like which you write, better you do not respond.

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Re: doubts on the process of molecular docking

nagaraj84
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In reply to this post by DANIHBK
Dear Researchers
I am Nagarajan.S from India. I have installed Autodock4 from long continuous attempt. Can any one please tell me What are the steps have to done before running Autogrid and Autodock.
I have tried more times but the results number of conformations not at all changing. All the 10 results are same .