Re: Re: Predicting the binding affinity and anion

From: Aron Broom (broomsday_at_gmail.com)
Date: Wed Nov 23 2011 - 12:46:33 CST

I'm not sure about the best way for the specific application of an ion, but
in general if you want to use MD to predict binding affinities (or free
energies of binding, as they are related), there are a number of methods.
I recommend you check out the NAMD 2.8 user guide under Biasing and
Analysis methods (http://www.ks.uiuc.edu/Research/namd/2.8/ug/node56.html).

I've done some Umbrella Sampling and MetaDynamics using a non-charged
ligand to a protein, and they both work well. Umbrella Sampling requires
more human input throughout the process, whereas Metadynamics only requires
you to think about the initial setup and then just let it run. If you
choose to go with MetaDynamics I suggest reading papers on the topic by
Parrinello who helped develop the method.

~Aron

> I have a designed some phosphate binding sites on my protein of interest
. I want to quantify the binding affinity between the phosphate ion and my
protein. I did some initial docking studies by focusing the > grid on that
region where the phosphate should bind. Now I want to make the prediction
more stronger using simulation or some other kind of method . I want to
know that how the binding affinity be
> calculated for interaction between a phosphate ion and a protein ?? Pls
help in this regard..

On Wed, Nov 23, 2011 at 8:23 AM, bharat gupta <bharat.85.monu_at_gmail.com>wrote:

> Hi,
>
>
> I have a designed some phosphate binding sites on my protein of interest .
> I want to quantify the binding affinity between the phosphate ion and my
> protein. I did some initial docking studies by focusing the grid on that
> region where the phosphate should bind. Now I want to make the prediction
> more stronger using simulation or some other kind of method . I want to
> know that how the binding affinity be calculated for interaction between a
> phosphate ion and a protein ?? Pls help in this regard..
>
>
>
> --
> Bharat
>
>

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