How can I compare the sequences of two protein chains from 2 different protein structures given in the Protein Data Bank in a residue per residue manner? For example, I would like to compare the alpha-tubulin sequences of 1TUB (from Sus scrofa) and 1JFF ( from Bos taurus). Are there any websites or software available with such a feature?
There are many tools and web servers to compare the AA or structure of two proteins.
To be specific - My favorite is T-Coffee webserver.
Link - http://tcoffee.crg.cat/apps/tcoffee/do:expresso (paste your fasts formats, you can also explore more according to your need)
After that you can redirect to JalView or EsPript from better visualization.
You can also utilize Pymol here.
If you wanna compare the proteins at their structural level. You can use Pymol or Maestro tools by superimposing one structure on another.
Syeda Rubaiya Nasrin, if you have some experience with R language and have RStudio installed on your machine, you can use the following script to perform a sequence-based structural alignment and superposition of the structures and save them in separate PDB files. Observe that you have to download the MUSCLE software executable and save it in a proper folder that have to be specified to the function file.path().
# Necessary packages
library(bio3d)
library(msa)
# File path to MUSCLE executable
file.path("D:", "Biblioteca", "R scripts", "Multiple Sequence Alignment",
"muscle3.8.31_i86win32.exe") -> fp.muscle
# Loading pdb files from Protein Data Bank
protein1
I usually use this website: https://www.ebi.ac.uk/Tools/msa/clustalo/
for sequence alignment. To compare protein structure I usually use Chimera, https://www.cgl.ucsf.edu/chimera/download.html
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