Comparison between structure of two protein PDB files

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2.3 years ago

Yoosef ▴ 60

I have two protein structures from I-tasser database which are normal and mutant forms of a protein. I would like to know is there a significant structural differences between two proteins with the ability of changing the protein function? I would be so pleased if you could introduce me a database to compare such PDB files.

folding pdb protein • 1.3k views

ADD COMMENT • link 2.3 years ago by Yoosef ▴ 60

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You could calculate the RMSD of the two structures in pymol and check where the structures differ the most. This won't tell you anything about the effects on the protein function, but it can give you hints for further investigations. To asses the effects of the substitution, you might want to look for dedicated software (PolyPhen2, SIFT, SAAP) or MD simulations.

ADD REPLY • link 2.3 years ago by fracarb8 ★ 1.6k

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Thanks for your help The Identified mutation is a 21 bp deletion in a highly repetitive DNA sequence. Does any of the databases you mentioned are able to predict the effects of such mutation? If not, I would be pleased if you could introduce a proper database for this purpose.

ADD REPLY • link 2.3 years ago by Yoosef ▴ 60

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