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I really appreciate @Matteo Ferla's detailed answer to my previous question.

I've already tested several tools to know if a mutation can cause a modification in the function of protein or not. There are some tools such as SIFT, PolyPhen 2, PROVEAN, SNPs&GO, I-Mutant, and so on. These tools give us the possibility to check if this mutation is deleterious or tolerant, So after using my own data on these tools I found that most of the tools give me ‘deleterious ‘ meaning that the structure of my mutated protein will be changed. So, my problem is about the mutated protein that does not have a PDB Code which I can use in Pymol, mcSm, SDM, DUET…. to visualize the 3d structure I tried to use BioPython but it requires a PDB code.

You talked about the swissmodel, I had tried to use this server but it gives me the same PDB code for the original protein and the mutated protein with a similarity of 100% and QMEAN approximately the same, as shown in the following figures:

enter image description here

After that, I had used this PDB code in PyMol but I didn't find the position 2700 in which the mutation occurs.

The ModeBase displays the same PDB code as Swiss-Model in which there is no 2700 position.

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enter image description here

The I-TASSER and EVFold require a small amount of data, since I am working on position 2700 these tools are not useful for me.

enter image description here

enter image description here

There is no method to visualize a 3d model with just a FASTA file or how to do my own PDB file based on a FASTA file using Python or R or any other language?

I have Fasta format data (not PDB code) which I would like to visualize in 3d structure using R or Python or anything that can help me because I can't use tools of 3d structure(i have not PDB code).

I've already tested several tools to know if a mutation can cause a modification in the function of protein or not. There are some tools such as SIFT, PolyPhen 2, PROVEAN, SNPs&GO, I-Mutant, and so on. These tools give us the possibility to check if this mutation is deleterious or tolerant, So after using my own data on these tools I found that most of the tools give me ‘deleterious ‘ meaning that the structure of my mutated protein will be changed. So, my problem is about the mutated protein that does not have a PDB Code which I can use in Pymol, mcSm, SDM, DUET…. to visualize the 3d structure I tried to use BioPython but it requires a PDB code.

As long as the mutation is not known yet, I couldn't use these tools because they need the PDB code that I haven't.

I would be grateful to those who will help me!!

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