[gmx-users] references on binding

Ran Friedman ran at hemi.tau.ac.il
Mon Jan 16 09:30:31 CET 2006


We've performed one such simulation with a lipid binding protein 
(Biochemistry 44:4275, 2005). We started with the ligand on the protein 
surface and ended with it being inside the protein, on the way to the 
active site (but not in the site). I doubt if you find simulations that 
really show the whole binding process due to sampling, unless you refer 
to very fast processes.


Diego Vallejo wrote:

>I would like to know about MD simulations of a protein-ligand binding
>process (not MD of complexes or  Free Energy Calculations, not steered
>dynamics, nor with pull springs, etc.)
>I mean a simulation starting from two molecules far apart and ending
>with the complex without artificial forces.
>Could you please pass the main references? (David, Erik,  Anton...?)
>Could be with gromacs or not.
>Thanks a lot.
>Diego Vallejo
>vallejo at iflysib.unlp.edu.ar
>diego.vallejo at gmail.com
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Ran Friedman
Laser Laboratory for Fast Reactions in Biology
Department of Biochemistry
Faculty of Life Sciences
Tel-Aviv University
Tel. +972-3-6409824
Fax. +972-3-6409875

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