Question: Energy minimization of protein
1
gravatar for chemistry1233
2.3 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 • 1.2k views
ADD COMMENTlink modified 14 months ago by ag1805x10 • written 2.3 years ago by chemistry123340
0
gravatar for ag1805x
14 months ago by
ag1805x10
India
ag1805x10 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 14 months ago by ag1805x10

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 9 days ago by prasundutta8770
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