Energy Minimization of protein structure

Question

[naeem.mahmood]

I have developed a 3D model of protein structure and minimized its energy through two different tools. After model refinement, I have checked energies of my models, obtained from two different tools. Interestingly, both models have shown a different type of structure after energy minimization and refinement. Why it so? I am a bit confused about it?

Answer 1

[natasha.sernova]

Energy Minimization In Protein Modeling

There are even more tools than you have found, some of them are below.

The first post shows that there is no right or wrong answer...

http://zhanglab.ccmb.med.umich.edu/ModRefiner/

"ModRefiner is an algorithm for atomic-level, high-resolution protein structure refinement, which can start from either C-alpha trace, main-chain model or full-atomic model.

Both side-chain and backbone atoms are completely flexible during structure refinement simulations, where conformational search is guided by a composite of physics- and knowledge-based force field.

ModRefiner has an option to allow for the assignment of a second structure which will be used as a reference to which the refinement simulations are driven.

One aim of ModRefiner is to draw the initial starting models closer to their native state, in terms of hydrogen bonds, backbone topology and side-chain positioning.

It also generates significant improvement in physical quality of local structures. The standalone program also supports ab initio full-atomic relaxation, where the refined model is not restrainted by the initial model or the reference model."

http://www.yasara.org/minimizationserver.htm

Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K Proteins. 2009;77 Suppl 9:114-22

http://spdbv.vital-it.ch/energy_tut.html

DeepView - Swiss-PdbViewer

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634918/

3Drefine: Consistent Protein Structure Refinement by Optimizing Hydrogen Bonding Network and Atomic-Level Energy Minimization

Different energy from different programs is not a surprise. - Different principles, different approximations -

there are too many features to vary.

Answer 2

[naeem.mahmood]

Thanks Natasha for your reply... Please let me know that is it essential to carry out energy minimization before conformational analysis of proteins?

[natasha.sernova]

See these answers below, it’s again ‘ I would say, it is necessary if possible,’

https://www.researchgate.net/post/Is_energy_minimization_required_if_i_use_PDB_models

But what tool will you choose? As you have noticed

different tools give different results. There is no best tool... I know about several good fitting programs, but it's too early.

( Energy minimization is definitely necessary before and after docking, but this is not your case:

https://www.researchgate.net/post/Is_energy_minimization_after_docking_necessary_before_running_analysis )

I know several good program for refinement, if you need them:

http://www.ysbl.york.ac.uk/~lohkamp/coot/wincoot.html

It doesn't require even stereo-glasses...

This tool, UCSF Chimera. It is free and it can do whatever you can imagine...

There are some examples of Rosetta.

https://www.phenix-online.org/documentation/reference/rosetta_refine.html