Question: Predicting Effect Of Mutations In Terms Of Activity
0
gravatar for Pappu
7.5 years ago by
Pappu1.9k
Pappu1.9k wrote:

I have a membrane protein (~400 aa) in which >90% of the mutations result in the loss of activity. I was trying to use SVM to predict the effect of mutation. However it predicts loss of activity in all cases. Let me know if it is possible to use PSSM matrices along with SVM or other tools to better predict the effect of mutation.

python • 1.5k views
ADD COMMENTlink modified 7.5 years ago by AsoInfo300 • written 7.5 years ago by Pappu1.9k
1
gravatar for AsoInfo
7.5 years ago by
AsoInfo300
Bonn, Germany
AsoInfo300 wrote:

You can try using project HOPE.

http://www.cmbi.ru.nl/hope/home

ADD COMMENTlink written 7.5 years ago by AsoInfo300

I don't think homology model will work because it is a membrane protein without any structural homolog. I have already tried homology/ab-initio modeling. But how can one validate such model most of the mutations are causing loss of activity?

ADD REPLYlink written 7.5 years ago by Pappu1.9k

You want to assess the biochemical effects of mutation in protein or you want to validate a protein structure using different tools?

ADD REPLYlink written 7.5 years ago by AsoInfo300

I want to assess the biochemical effects of mutation in protein.

ADD REPLYlink written 7.5 years ago by Pappu1.9k
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