Question: Energy minimization of protein
1
gravatar for chemistry1233
3.2 years ago by
chemistry123340 wrote:

It`s neccesary to minimize energy for protein before docking ( docking with autodock vina), and what to use for this, what software to use, I dpwnload protein PDB from rscb.org and then remove before ligands and water with discovery studio and then add polar hydrogen and kollman charges throught autodock tools(convert to pdbqt file). I am asking if I need to minimize energy of protein, where do I need and what to use for thisĀ 

software error • 1.6k views
ADD COMMENTlink modified 2.1 years ago by ag1805x80 • written 3.2 years ago by chemistry123340
0
gravatar for ag1805x
2.1 years ago by
ag1805x80
India
ag1805x80 wrote:

I have the same question. I have modelled my protein using PHYRE2. Do I need to do energy minimisation before docking?

ADD COMMENTlink written 2.1 years ago by ag1805x80

Swiss-PDB Viewer can be used for energy minimization- http://spdbv.vital-it.ch/energy_tut.html Reason mentioned in the tutorial..

ADD REPLYlink written 11 months ago by prasundutta87170
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