Program for DNA sequence to structure conversion - (Mar/21/2006 )

Hi everyone,

I'm facing the following problem. I have a known DNA sequence and want to have a .pdb or similar to depict it. So, I like to have a helical DNA with my basesequence. Does anyone have an idea, if there is a program which can do this, or a way how to achieve this?

Thx, Kersten

Erm right then...
I assume you have checked to see that there is indeed no structure file for this DNA sequence? If not have a look at the ensembl database hosted by the EBI, is tends to have links to other databases such as the PDB.

If not then:
you have 2 choices. Search for known structures using the sequence to see if you can identify things that are like your sequence.
or and more fun
build a model. If you can find a suitable homolog then you can use the swisss deepview program to automagically build a model which 'may be similar to the structure your protein sequence adopts.

The quality of such a model would depend upon the quality of a sequence with known structure you (swiss view) finds


If however you are after a DNA structure - no idea.

yeah .. i'm after the DNA structure, that's my problem but thx for the reply anyway. can swissprot model DNA? i don't think so ... is there any other program? maybe this ballview? i don't know all these programs

This database may interest you:

http://ndbserver.rutgers.edu/

Best of luck,
Hank