Any script that can produce different mutations of protein sequences at specified positions?

Question

[maa4618]

Hello :)

I want to ask if there is a Python script or any other languages that can undergo the task shown below or something similar.

The task:

Input --> Wild-type (WT) protein sequence and indicate positions where you want mutations to occur.

Output --> Generate several sequences with different permutations using the 20 amino acids at these specific positions.

Thanks.

[Ernest Bonat]

i know if we have any python script for this task. if you can post an example, i can look at it and provide some python code ideas how to do it.

[LauferVA]

I'll bite! what kind of ideas??

[maa4618]

Yeah sure for example:

Input

1. WT protein sequence: "MSQKQTPLKLNRFQGISIVAN"
2. Want to mutate at position 2 and 4 from the sequence as denoted by X "MXQXQTPLKLNRFQGISIVAN"

The Output are mutated sequences at positions 2 and 4 with the 20 amino acids:

• MAQAQTPLKLNRFQGISIVAN
• MGQAQTPLKLNRFQGISIVAN
• MAQGQTPLKLNRFQGISIVAN
• MGQGQTPLKLNRFQGISIVAN
• MFQPQTPLKLNRFQGISIVAN

There should be around 20^2 combinations

[fracarb8]

You can use rotkit.mutate in pyMOL. The basic command should be mutate(molecule,chain,resi,target,mutframe) .

Answer 1

[Mensur Dlakic]

Almost all protein design programs can do what you asked. Some of them are python-based, such as PyRosetta . There is also a server where you can try this program without investing time to learn its programming structure.

http://rosettadesign.med.unc.edu/

SCWRL4 can do quick "mutagenesis" by shuffling through residue rotamers from a predefined library.

[GenoMax]

resettadesign server linked above appears to be no longer available.

[LauferVA]

Just looked into this - @Mensur is it subsumed by the PyRosetta Link above it?

[Mensur Dlakic]

I used the design server some years ago, but don't know why it doesn't work or if it migrated elsewhere. Without logging in, it seems that the main page is still there.

[GenoMax]

Interesting. The server was not working when I checked earlier but it seems to be now.

[LauferVA]

sorry for adding to the confusion gentlemen. on the bright side, i did not know it existed and will now go play with it :-D