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?
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.
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.
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Similar question: Energy minimization in protein modeling
Energy minimization with that of AMBER and CHARM M are diferent??? How and which one is better to use?
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.