Question: Problem With Ramachandran Plot
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gravatar for Dollas Salleh
5.0 years ago by
Besut
Dollas Salleh70 wrote:

A)Ramachandran Plot

Residues in most favoured regions 83.6%

Residues in additional allowed regions 11.6%

Residues in generously allowed regions 3.4%

Residues in disallowed regions 1.3%

B) G-factors Dihedrals: -0.63 Covalent: -0.07 Overall: -0.38

# I have already built 3D structure of my target protein. And go through some validation like the Ramachandran plot as shown above.

My problem is

1) Can I accept the 3D model that has been built. Because?, according to the literature that I has studied. They said a good quality model would be expected to have over 90% in the most favoured regions.

2) For G-factors, according to literature The overall G-factor quality was 0.2, indicating a good quality model (G-factor values between 0 to 0.5 are acceptable) but i get -0.38 .

Anybody who has experience for that above matter? I need help.

plot • 1.9k views
ADD COMMENTlink modified 4.9 years ago by Neilfws47k • written 5.0 years ago by Dollas Salleh70

If you want to validate a homology model, there are much better tools that Ramachandran plot. Try ProQ, Modfold and Prosa.

ADD REPLYlink written 4.9 years ago by Pappu1.8k

Dear Pappu. Sorry for the late reply, Thaks a lot. Tools that you have provided help me a lot. Thanks once again Pappu

ADD REPLYlink written 4.9 years ago by Dollas Salleh70
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