I would try I-TASSER, which creates 3D models based on multiple alignment throughout the PDB. If you add "Bioinformatics and Computational Biology" and "Structural Bioinformatics and Computational Biology" to the topics (instead of "alignment" and "multiple alignment" you will get many more answers.

http://zhanglab.ccmb.med.umich.edu/I-TASSER/about.html

Try UCSF Chimera - also a great molecular modelling program.

Chimera also has the very handy feature of being able to create a structure-based sequence alignment - that is, to align two or more structures, then create a sequence alignment based on which residues in each structure are aligned structurally.

Also, if you load a multiple sequence alignment into Chimera, you can color the structure by conservation, which I have found useful on multiple occasions.

http://www.cgl.ucsf.edu/chimera/

I'm using Expresso http://tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi

http://tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi

Hi, so in fact if you want to use the structure to guide your alignment you need more than one structure. For instance using Expresso (structural mode of T-Coffee), it will fetch and use all the available structures for your sequences (structure with enough identity to your sequences). It might help you to identify other related structures without to perform the BLAST against PDB yourself. What you can also do is to use the single structure you have to assess the quality of alternative alignment using an option of T-Coffee (STRIKE Bioinformatics. 2011 Dec 15;27(24):3385-91). You can give it a try using the webserver if you don't specially want to install T-Coffee and run command lines (http://tcoffee.crg.cat/apps/tcoffee/index.html in the section evalution).

If you want just to map the structure onto the alignment then you need visualizing tools, probably Jalview might be of help for this.

Hello,

Thanks for the replies. They are great suggestions!

Best,

Nanda

Hello,

You can also use Espript or Endscript.

You will obtain a multiple alignment adorned with the secondary structure elements of the crystal structure.

http://espript.ibcp.fr (input is a clustalw output)

http://endscript.ibcp.fr (input is PDB id)

please read also the tutorial for beginners and advanced users ;-)

http://espript.ibcp.fr/ESPript/ESPript/tutorial.php

cheers

patrice