online software availability

Question

[jananinithu]

Hi,

I have a protein sequence and I need to mutate a sequence without changing the folds. Is there any tool available to check which amino acid residues in protein sequence can be mutated?

[Michael]

Please edit your question to contain enough detail to answer it. What do you mean by: "mutate a sequence without changing the folds". I guess you mean "which residues can be mutated without changing the structure of the protein (too much)"? What is your application of knowing these unconstrained residues?

[Ibrahim Tanyalcin]

I think he wants to get a list of possible SNVs at a position from the given codon in the cDNA so he doesnt have to go through the ones that aren't biologically possible for an SNV.

[Michael]

Like all synonymous codons? Certainly, that would keep the protein sequence identical.

.....Maybe.....

[Michael]

Btw.: If it's this I would use a chain of EMBOSS tools: transeq | backtranambig, that should output all ambiguous nucleotide sequences. However, if the application to express recombinant protein, it would be better to use backtranseq with a proper codon-frequency table.

Answer 1

[Ibrahim Tanyalcin]

Which protein are you interested in? I have couple graphs where you can check that, if I have the one you are looking for maybe I can help

[jananinithu]

oph is the protein sequence

[Ibrahim Tanyalcin]

Sphingopyxis sp. (strain 113P3) with Uniprot ID of Q588Z2 ?