Hi Alessandra,
Here is a list of nucleic acid and protein-nucleic acid related tools
(including the ones mentioned by Luca and Maia:
3DNA
http://rutchem.rutgers.edu/~xiangjun/3DNA/
http://w3dna.rutgers.edu/
curves
http://gbio-pbil.ibcp.fr/Curves_plus/Curves+.html
nucplot
http://www.biochem.ucl.ac.uk/bsm/nucplot.html
protein-nucleic acid interaction server
http://www.biochem.ucl.ac.uk/bsm/DNA/server/
freehelix
ftp://ndbserver.rutgers.edu/NDB/programs/freehelix98/README
In addition, general analysis tools might be useful as well:
difference distance matrix
http://www.roselab.jhu.edu/ddmp/
moleman2 (distance commands and others)
http://xray.bmc.uu.se/usf/xutil.html
lsqman (plots; superpositions of nucleic acids possible, "at ph" or
define your own atom type)
http://xray.bmc.uu.se/usf/dejavu.html
...
Best regards,
christian
Alessandra Pesce wrote:
> Dear All,
>
> I am looking for available programs and/or websites able to check the
> structure of DNA in DNA-protein complexes. I need to evaluate the DNA
> bending, its backbone distortion, the alteration of the base pairing,
> and its interaction with the protein. The aim is to compare in easy and
> quick way different conformation of DNA in different DNA-protein
> complexes. Can anybody help me?
>
> Thanks in advance.
>
> Cheers
>
> Alessandra
>
>
> *************************************************************
> Alessandra Pesce, PhD
> Department of Physics
> University of Genova
> Via Dodecaneso 33
> 16146 Genova, Italy
>
> Tel.(DIFI) ++39 010 353 6243 | 6309
> e-mail [log in to unmask] <mailto:[log in to unmask]>
> *************************************************************
>
--
_______________________________________________________________________
Dr. Christian Biertümpfel
Laboratory of Molecular Biology
NIDDK/National Institutes of Health phone: +1 301 402 4647
9000 Rockville Pike, Bldg. 5, Rm. B1-03 fax: +1 301 496 0201
Bethesda, MD 20892-0580
USA
_______________________________________________________________________
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