Condel Is a method that gives combined score of polyphen, SIFT etc.
Prediction Of Mutation Impact
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.
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Shicheng Guo
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kylejudita •
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kylejudita •
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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
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kylejudita •
Maybe the same features as described in the publications listed here?
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Michael Dondrup
Sorry for the misunderstanding, with here I meant in the respective publications of the tools found in the answer by Rm given above. In principle, choosing the same features as SIFT of Polyphen.
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Michael Dondrup
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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Shicheng Guo
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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.