Hi,

The best conformation given to you by the docking program, i.e minimum energy of the protein-ligand complex and maximum binding affinity should be selected for molecular dynamics study. It would be better if you can perform MD simulation on all of the 240 poses because when we perform docking it is in the vacuum conditions so the "best" conformation that we receive is only hypothetical, so as to confirm the best pose we have to study the effect and dynamics of the system in different solvent system and after MD simulation you will have an idea about which complex is stable. Hope that this helps you.

Danish J

You can perform program for minimum energy and maximum affinity in the protein-ligand complexes. Once you find the docking partner(s) from the above, you can check for the interactions like H-bond distances, ionic interaction etc to choose the best one.

I agree with Danish Jasnaik, I may give some more idea. As the simulation should work into  a solvant, I suggest to test the found energies with water in some structures that could be changed with water molecule interaction. In some binding water could participate to the energy. Morever, some water molecule could be found as a strategic part of the global binding. Have a look to this aspect of interactions. Hoping that help a bit.

Yves Chapron

You might try different computational scoring function and then try a consensus between them. Or if you have NMR data on the complex, for instance chemical shift perturbation, you can try to apply this approach: http://pubs.acs.org/doi/abs/10.1021/jm701194r

you can perform according to the minimum binding energy and maximum binding affinity