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automated protein structure search - (Apr/06/2009 )

Hi all, I have a short aminoacid sequence that I know is found in quite a few protein structures in PDB. and I want to know where it is located in these structures. like is it on the surface, in the core, on the C terminus etc. this is probably a long shot but does anybody know a tool that I can use to search these structures automatically (there are a lot!) instead of going through them one by one and testing by eye? thanks..



-Minnie Mouse-

Minnie Mouse on Apr 13 2009, 10:54 PM said:

I don't think blast can show whether a particular sequence is located in the core or surface of a protein.


You are right, it can't. As you have plenty of structures you could use a tool like NACCESS by Andrew Martin @ ucl (I think) to measure the solvent accessibility and make a decision as too how buried or exposed the section of protein is. Alternatively, download the DSSP file for that protein and look at the solvent accessibility there (given as an absolute solvent accessibility but you can change it to relative solvent accessibility using a conversion table).

* There are tools out there to parse DSSP files - I may even have some python code for you if you opt for that route.

thanks a lot for the reply. it was helpful. I think NACCESS requires linux. I have a windows machine. so I looked at the some DSSP files. is it the ACC column that shows the solvent accessibility?

I am also thinking maybe pymol can do the same. ideally what I'm trying to do is find a way to enter a txt file that lists 300-400 PDB id's as the input and get a solvent accessibilities for each of them as the output. (so that I don't have to enter each structure one by one)

If you have the python code that I can use to extract solvent accessibility from DSSP files I think I could use it. thanks again.


do you already have the pdb files?

I have a script that will run off and get the pdb files and the dssp files at the same time.

I am about to format my machine - will post the code later.