Visualize a Superimposition of Two Protein Structures Using a Sequence Alignment as Input

Question

[joseph.luttrell]

Hello everyone,

I have two PDB structures and a preexisting alignment of their sequences that I generated with a program that i'm working on. What I want to do is input this alignment into UCSF Chimera or PyMol (or any other structure visualization software) and generate an image with the two protein structures superimposed according to this alignment. Is there a tool that does this or should I attempt to write something myself? My only idea involves writing a script that will edit the pdb files so that the 3d coordinates of the aligned residues are within a certain distance of each other. However, this is probably too simple and might create weird stretching or other effects?

Answer 1

[Jean-Karim Heriche]

The RSCB protein comparison tool allows you to do this although it doesn't allow you to input your own alignment (you have to select an alignment method). The standalone program seems to be available here. You can also try your luck with other pairwise structure alignment tools. For example, UniAlign (paper) may be doing what you want although the web site also doesn't allow you to input your own alignment. Note that it looks like pairwise structure alignment under distance constraints is NP-hard.