I want to perform docking of a protein with a small molecule caffeine. I had missing residues in my protein which I modelled through modeller. After going through many literature, I found that MD based minimization is necessary for a protein before docking if missing residues have been added to it. When performing MD simulation of the protein till minimization step, using Amber, we get an output file (say protein_wat_min2.pdb). Can this pdb be used in autodock directly for docking. Can this structure be considered as our minimized structure. If yes, Can anyone tell me what necessary modifications has to be made on this file to use it in autodock as the receptor.
Aziza Rahman
You can minimized by Yasara, Galaxyrefine, Spdbv, Gromacs etc.
It is necessary to model those residue missing in the pdb file, unless they are really far away from the docking binding-site. Trying to keep experimental information, but dealing with the new modelled side chains, you can only minimize the modeled residues. Then you can proceed with docking.
Before performing energy minimization of your modelled structure , check whether the missing residues falls in the active site/catalytic site...In that case u must do modelling ( using multiple templates in modeller )..then validate your modelled structure using WHATIF web interface, ProTSAV, Prosa etc., then go for energy minimization...
In Removing all the known amino acid residue in your crystal structure,you mistakenly deleted something,but you can use SPDV to do the minimization
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