Question: Homology Modelling And Energy Minimization
0
gravatar for tithiroy33
5.8 years ago by
tithiroy330
Bangladesh
tithiroy330 wrote:

I have done homology modelling using Modeller. what is the relationship between energy minimization and modelling? Is it essential to minimize the energy after modelling?

homology • 2.8k views
ADD COMMENTlink modified 24 days ago by manishagurnani100 • written 5.8 years ago by tithiroy330

Similar question: Energy minimization in protein modeling

ADD REPLYlink written 5.8 years ago by Neilfws48k

Energy minimization with that of AMBER and CHARM M are diferent??? How and which one is better to use?

ADD REPLYlink written 24 days ago by manishagurnani100

Hi manishagurnani10,

as in this thread A: Ab Initio Modelling Of Small Protein please do not ask questions in old threads. Please follow the advice given in the linked thread on using the search/google and then posting a new question.

ADD REPLYlink modified 23 days ago • written 23 days ago by ATpoint17k
2
gravatar for João Rodrigues
5.8 years ago by
João Rodrigues2.5k
Stanford University, U
João Rodrigues2.5k wrote:

When you do homology modelling, you basically replace the residues on the template with those of the sequence you are modelling. Each modelled residue is inserted in a complex environment and needs to 'adapt' to it This is what energy minimization is there for. Imagine that you have a tryptophan residue being modelled where a glycine was in the template. For sure you'll have some steric clashes due to the larger size of the tryptophan, the side chain interactions in the vicinity need to be readjusted, etc. Energy minimization simply brings the system to a point of lower potential energy, thus more stable, and is used to clear up these issues.

Energy minimization will rarely 'ruin' your model, it will usually clear up some bad stereochemistry, but it won't do miracles.

ADD COMMENTlink written 5.8 years ago by João Rodrigues2.5k

Very nice comment!

ADD REPLYlink written 5.8 years ago by Cacau430
1
gravatar for Cacau
5.8 years ago by
Cacau430
Canada
Cacau430 wrote:

http://zhanglab.ccmb.med.umich.edu/ModRefiner/ ModRefiner is a good tool to minimize the energy of your model. You can also see many useful tools developed by the same group on this webpage.

ADD COMMENTlink written 5.8 years ago by Cacau430
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