Hi,
am trying to "predict the effect of mutation impact on protein function", am trying to get features to achieve the prediction. I wonder what features I can get using BLAST, BLAST-PSI. I have data for protein sequence, mutation, position of mutation.
To "predict the effect of mutation impact on protein function": look for servers like polyphen, SIFT, PolyDoms etc...
Using SIFT and PolyPhen to predict loss-of-function and gain-of-function mutations
Thanks, but I still need to find the features, . What features I need to include if , for example, I want to predict the effect of mutation on protein function . I guess it is a matter of experimentation, but there must be a number of features must exist. I currently have WPM, wildtype residue, position, Mutation residue, and protein sequence. I see many papers use Blast, what features I can get when calling Blast? Thanks
Hi!
As Rm suggested, you can use SIFT, PolyPhen, I-mutant, CUPSAT, CONDEl etc.
It all depends what you want as an end result and the approach you want to adapt.
AlphaFold V2 increase protein 3D structure prediction accuracy to next level (~90%). AlphaFold received a very high score which is around 90, even for some worst situation, distance score test come up to 80+. You can try to take genetic variants into the model and check what will happen to the new 3D structure. https://deepmind.com/research/open-source/alphafold_casp13
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This appears to be an almost identical question to your original post: http://www.biostars.org/post/show/48786/blastpgp_mutant_residue and your follow-up question which was deleted as a duplicate: http://www.biostars.org/post/show/48840/looking-for-features-to-predict-mutation-impacts/. Please stop posting the same question.
As Neil said. Just in case you don't know, you can edit your question or post comments to answers if they are not satisfactory to you, but chain posting doesn't help your cause at all.