Hi,
I want to get an idea of the structure of a protein which structure has not been determined as of now. However, I know of a protein that shares two conserved amino acid motifs, which I want to use as a template for homology-based structure prediction using MODELLER.
The two motifs are 100 amino acids apart from each other.
My question is:
What is the best/standard way to have both conserved motifs matched with each other and the remaining residues aligned as per usual?
thank you!
Best,
Michael
If you have the pdb file of your protein template. Just extract these two motifs using any text editor, save them as separate pdb files and align them using pymol.
Following link will be of help:
http://pldserver1.biochem.queensu.ca/~rlc/work/teaching/BCHM823/pymol/alignment/
In some cases like this when we try to align regions around matchingsi have used dialing
what I ended up doing was manually aligning the conserved motifs and than aligning the surrounding sequences with the MODELLER algorithm which worked out nicely.
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