[Dock-fans] Internal Energy

Sudipto Mukherjee sudmukh at yahoo.com
Tue Sep 8 14:22:27 PDT 2015


Hi Sneha,
>From the manual:
>The goal of the internal energy function is to reduce the occurrence of internal clashes during the torsional optimization. >This function computes the repulsive Lennard-Jones term between all ligand atom pairs, excluding all 1-2, 1-3, and 1-4 pairs. 

The internal energy function was never meant to be used for ranking ligands by binding affinity. Rather this is a way to prune unphysical small molecule conformations while growing torsions. Importantly, this does not include attractive VDW, Coulombic or torsion terms.  Regards
Sudipto Mukherjee 


     On Tuesday, September 8, 2015 5:14 PM, William Joseph Allen <william.joseph.allen at gmail.com> wrote:
   

 Hello,
I am not sure if you have gotten a reply yet, we are having a problem with out mailing list server at the moment.
The answer to your question is no. A lower internal energy (closer to zero) does represent a more favorable conformation of the molecule, but it does not consider the molecule's interaction with the receptor. If you had two poses with equal interactions with the receptor, but different internal energies, we would generally call the pose with the lower internal energy 'more favorable'. But, it is still a stretch to relate that directly to binding affinities.
Joe Allen
On Mon, Sep 7, 2015 at 3:20 PM, Sneha Poondru <snehapoondru at gmail.com> wrote:

Hi All,

I was trying to search the archives, but none of the messages are opening. My quick question is, do lower Internal Energies mean better binding affinities?

Thanks!
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