I am trying to find out the binding energy of metal ions to a proteins.
I have identified the metal ion binding site of that protein by using MIB : Metal Ion-Binding site prediction and docking server.
I there any DFT methord or MM methord to find the binding energy?
For 3D Structure and Cavity you can use:
CASTp, Autodock vina, Swissmodel, Qsite, Chimera, RasMol or JMOL, MOE, BIOVIA Discovery Studio.
.
I-Tasser is for predicting protein structure
The binding will be dominated by electrostatic interactions.
1. Choose an approach which can reproduce the solvation free energies of your ions.
2. Choose an implementation of the approach.
Beware of 1-click solutions.
Hi, why did you identify/predict the binding site in protein? Is there no experimental report that this metal ion binds to these residues.
As Martin Klvana stated that the binding will be dominated by Electrostatic interactions and Elect are long range in nature. I am also stuck with this kind of situation where the interaction spans the entire protein and most of the residues (for electrostatic interactions).
For solvation free energy, you can use a web server our lab developed based on 3D-RISM method:
https://www.prowave.org/solvation-free-energy/
As and additional literature, the following paper can be helpful:
https://www.pnas.org/content/pnas/102/29/10147.full.pdf
Good luck
Elect are long range in nature - Electrostatic interactions are short range in nature.@Muhammed
Nikhil Maroli , at the molecular scale, electrostatic interactions are long-range (especially in the case of charged entities): for this reason, no cut-off should be used for electrostatic interactions between the ligand and the rest of the simulated system for accurate calculation of the solvation free energy.
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