Should energy minimization of native and mutant protein structures be done before RMSD calculation between these two?
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3.9 years ago ▴ 30

I want to calculate the RMSD values between a native protein and several of its mutant structures. I did energy minimization of them by YASARA minimization server after modelling through MODELLER v9.23. Now I want to use YASARA view for RMSD calculation. Is it better to calculate RMSD between native and mutant structures after energy minimization? Or can I calculate RMSD directly after building models? Do 'energy minimization' and 'RMSD' calculation have any correlation with each other or they can be separately done independent of each other?

Homology RMSD Energy Minimization YASARA • 982 views
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Should calculate RMSD between the non-optimised and then between the optimised structures and report both. From experience (albeit from a long, long time ago), the RMSD of the optimised structures can be worse. Remember, that the optimisation can only be as good as the quality of the force field parameters used, and may introduce artefacts.


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