I have looked into Cn3D but they only visualize solved crystal structures in databases.
I have recently been trying to compare protein sequences of a working stock of virus to the protein sequences of the master stock to check for mutations.
The genetic sequences were compared, mutations found, and then I translated the DNA sequences to protein using Expasy.
However, BLASTp only shows the sequence differences and I was hoping to model the mutated protein structure and compare it to the unmutated master stock proteins.
I have looked into Cn3D but they only vistualize solved crystal structures in databases.
Are there any programs available where you can input an amino acid sequence and get a simulated 3D structure?
Hello Jasmine Mueller
Basically, what you are looking for is a software that can model your sequence into a protein 3D structure.
I personally used MODELLER ( https://salilab.org/modeller/download_installation.html ) it is free and can be installed in multiple OS.
Other web-based tools for protein modelling:
- I-TASSER ( https://zhanglab.ccmb.med.umich.edu/I-TASSER/ )
- SWISS-MODEL (https://swissmodel.expasy.org/interactive)
Hope this helps. All the best
You may utilize the Swis-Model server for homology modeling of your protein. While UCSF-CHIMERA is useful to compare the protein structure models.
I agree with the Farrah Wahidah Ridzwan. Further you have to go for molecular dynamics simulation.
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