[gmx-users] the effect of ligand on protein

[ahmet yıldırım]

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

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Ahmet Yıldırım