I have to perform molecular docking on 2 ligands (A structure-absent in literature and B structure-sourced from PubChem) therefore, is energy minimisation necessary for both?
Hello! Having an energetically minimized starting PDB structure is always useful, as it eliminates a series of issues that may arise when performing docking and subsequent molecular dynamics.
It would be helpful to perform energy minimization on the structure not sourced from PubChem, especially since it is not present in the literature and therefore needs to be characterized upstream for further study. For ligand B sourced from PubChem, while it may have a known structure, I think that a energy minimization can still be beneficial for refining its conformation and ensuring compatibility with the protein target.
Hope this helps! :)
Yes. Energy minimization is a geometry optimization technique which brings the molecule in more reliable conformation. It is an essential step before carrying out any further molecular modelling calculations. It removes if any steric clash is there and also optimizes the favorable interactions. That means it helps to bring the molecule/system in local minimum conformation/configuration by minimizing the repulsive forces and maximizing the attractive forces. It is calculated as a negative gradient of potential energy.
use this app which automatically energy minimized the ligands while preparing https://sourceforge.net/projects/mzdock/
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