[gmx-users] Re: the effect of ligand on protein

[ahmet yıldırım]

Dear users,

any suggestion?

Thanks in advance

2012/7/2 ahmet yıldırım <ahmedo047 at gmail.com>
>
> Dear users,
>
> Which analysis do you suggest to examine the effect of ligand on protein?
>
> 1.)For quality assurance:
> RMSD,RMSF and Radius of gyration for free and complex form
>
> 2.)For structural analysis:
> ISA (interface surface area), the number of hydrogen bonds between
> protein and ligand, secondary structure for free and complex form
>
> 3.)Principial component analysis:
> The eigenvalues versus the first 30, 40 or 50 eigenvectors
> Projection of trajectory onto onto the first five or ten eigenvectors
> Projection of trajectory onto the plane of first two eigenvectors
> Cosine Content of some eigenvectors
>
> Are these analyzes adequate?
>
> Thanks in advance
>
> --
> Ahmet Yıldırım




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Ahmet Yıldırım