Structure based multiple protein alignments - How can I improve my alignments if I have a partial structure? (Dec/02/2006 )

Hello,

I would like to improve my protein sequence alignments. I have partial structures for two of the proteins. Can I use these structures in combination with the alignments to produce better alignments? I heard that TCoffee can do something similar, but I am not sure.

Any suggestions?

Gimel

you should try jalview, for secondary structure prediction

ermmm you can do a sequence structure alignment. Try using DALI at the EBI it should be able to do the trick (that would be structure structure). TCOFFEE, I think, came from this lab but no one uses it as far as i am aware...

TCoffee can indeed do it, using their Expresso program:
http://www.igs.cnrs-mrs.fr/Tcoffee/tcoffee_cgi/index.cgi

Try www.expasy.ch for the structure alignment applications.

Or, you could get the best primary sequence alignment, and see if the structure has been done. If so, go to the protein database, and see if quickpdb will thread your sequence onto the known one.