Homology Modelling Steps

Question

[Zak]

Hi all I have recently started a training in homology modeling using modeller, I modelled a protein structure and performed model validation through SAVES , Procheck showed that some of the amino acid residues were in disallowed region.. To correct it i was told to build loop using spdbv tool so that the reidue could be draged into allowed region. I have doubts regarding this step..

1. how can we decide that the residue has to go into allowed region ?
2. once build loop is done ,won't it change the shape and orientation of the protein and its residues ?

Can u also help me regarding how to perform energy minimization.

thanks in advance !!!

Answer 1

[Anuraj Nayarisseri]

Here is the basic Homology Modeling steps by Modellar. If you have any queries from this step pls post again. http://salilab.org/modeller/tutorial/basic.html

[Keith Callenberg]

It seems that the poster has already followed these steps or something similar. He is looking for help with refining a model he has already built.

Answer 2

[Vladimir Chupakhin]

1. If the residues with bad geometry in the regions you don't care - skip them. For example if you are building the models for protein-protein docking or ligand-protein docking and the residues far from the binding site or interaction interface
2. Strange question :)
3. Modeller have minimization routine, also try Gromacs, Chimera have some minimization procedures.

[Zak]

thanks chupvl :D

for my second i meant that ramachandran plot is according to psi/phi values if we are changing them ,won't this affect the structure...