Question: Energy Minimization In Protein Modeling
8
gravatar for Pals
7.7 years ago by
Pals1.3k
Finland
Pals1.3k wrote:

I am a beginner in the field of structural bioinformatics. I have done some modeling projects however I am always confused in minimizing the modeled structure. One of my teachers told me to minimize the modeled structure after generating the final model. On the other hand, another instructor with whom I did modeling project did not recommend me to minimize the modeled structure. He told that it is worthless to minimize the modeled structure as the structure has already suffered a lot of constraints as it was built using the template structure. In that case, the conformation of the minimized structure will be worse than before. Both fellows tried to convince me in their own respect but still I am confused myself. Could anyone please clarify this so that I will decide whether or not to apply this step in modeling my proteins.

protein structural • 6.7k views
ADD COMMENTlink modified 7.7 years ago by BioDiscovery0 • written 7.7 years ago by Pals1.3k
7
gravatar for Anuraj Nayarisseri
7.7 years ago by
Indore
Anuraj Nayarisseri740 wrote:

Some applications will automatically perform energy minimization while modeling the protein. some applications we have to do manually energy minimization. But Its a mandatory to perform energy minimization as its included in the protocols of Comparative modeling.But let me know which application you used for modeling. If you are using SPDBV for modeling you have to perform energy minimization. If you are using ICM Molsoft which is a commercial tool it will automatically perform Energy minimization while modeling.

ADD COMMENTlink written 7.7 years ago by Anuraj Nayarisseri740

I have been using Modeller.

ADD REPLYlink written 7.7 years ago by Pals1.3k

Hai...iam using modeller9.19 for homology modeling,for energy minimisation of my protein which software is better for my resulted model?

ADD REPLYlink written 12 months ago by ramyajadhavm0
4
gravatar for Spitshine
7.7 years ago by
Spitshine630
Esch-sur-Alzette, Luxembourg
Spitshine630 wrote:

There's no wrong and right here. Although I side with those that consider minimizing the energy heavily subsequently to do more harm than good, it certainly depends on the condition, model and structure and your actual question. It'll take quite some experience to learn those conditions. Be merry and take it on your list of open questions.

ADD COMMENTlink written 7.7 years ago by Spitshine630
4
gravatar for Jan Kosinski
7.7 years ago by
Jan Kosinski1.6k
Jan Kosinski1.6k wrote:

It depends what you need your model for. If you build your model to interpret some experimental data, or to check which residues are exposed to solvent, etc. you don't need to run any minimization - it will not change the model much: even if you get improvement of the model quality, the improvement would be marginal, and will not change your answers.

But if you plan to use a model for docking, minimization may be good idea. But try to do constraint minimization, so that residues conserved between model and template do not move.

If your model comes from SWISS-MODEL or Modeller, and does not contain severe errors (like knots or wrongly placed indels that cause backbone passing through the protein core), it will not have clashes and the minimization would not harm. If you see backbone clashes, try to remove them by changing the target-template alignment. If you see side chain clashes, try to remove them using a program like SCWRL (again, in a mode that preserves the conformation of conserved side chains).

ADD COMMENTlink written 7.7 years ago by Jan Kosinski1.6k
2
gravatar for Mndoci
7.7 years ago by
Mndoci1.2k
Issaquah, WA
Mndoci1.2k wrote:

As others have suggested, there is no hard and fast rule, since it depends on so many factors. I've always chosen to do some gentle minimization to remove clashes. With Modeller you probably don't need much more.

ADD COMMENTlink written 7.7 years ago by Mndoci1.2k
0
gravatar for Amit
7.2 years ago by
Amit0
Amit0 wrote:

i think it will help to a certain extent....i always minimize the energy for better structure

ADD COMMENTlink written 7.2 years ago by Amit0
0
gravatar for BioDiscovery
6.4 years ago by
India
BioDiscovery0 wrote:

Energy Minimization can repair distorted geometries by moving atoms to release internal constraints

ADD COMMENTlink written 6.4 years ago by BioDiscovery0
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