Question: Energy Minimization To Determine Backbone Clashes
gravatar for Harpalss
7.9 years ago by
Harpalss310 wrote:

I am currently modelling a protein, I have so far generated 160 models of this protein.

I then remve models that have backbone clashes via energy minimisation. Models with a -ve energy after minimisation were considered to have no clashes where as proteins that have +ve energy after minimisation were considered to have a clash.

I then looked at structures that had -ve energy and some of them had severe backbone clashes, where as other model with a +ve energy did not.

Is there any reason for this? Which is the best way (rather than eye) to determine if a protein has a clash?

I performed minimisation in Chimera. I did 100 steps, with 0.02 angstrom movement and no fixed atoms.

Also, is it better to look at the energy or the gradient norm? I used energy because I do not know what the gradient norm is.

ADD COMMENTlink written 7.9 years ago by Harpalss310
gravatar for João Rodrigues
7.9 years ago by
João Rodrigues2.5k
Stanford University, U
João Rodrigues2.5k wrote:

How are you modelling the protein? I am surprised that a lot of people use Chimera and Pymol to model proteins when their function is strictly graphical.. If you are modelling something, I would recommend you to use MODELLER, or I-Tasser if homology is low.

Well, energy minimization MIGHT get rid of all the clashes, but it depends on how strong the minimizer is and for how long it runs. Download GROMACS, install it, and run energy minimization until machine convergence. That is much longer than 100 steps and might fix more clashes. Also, use WHATCHECK or another software like that to check for stereochemistry of your models instead of just looking for clashes.

ADD COMMENTlink written 7.9 years ago by João Rodrigues2.5k
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