Is it necessary to minimize homology model for docking and cavity volume studies?

Question

[mallikav]

Hi

I wish to study the substrate binding pocket volume, area etc.

Also protein-small molecule interaction studies ..

the protein modelled via swissmodel-automated mode..(template-target similarity 94%)

What method you suggest in order to get a clear picture of structural studies.

How molecular dynamic simulation will help my studies?

I also wish to go for some quantum mechanics approach.

As a beginner in this field, it will be very helpful, if u can give some suggestions.