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 pe...@ge.infm.it <mailto:pe...@ge.infm.it> > ************************************************************* > -- _______________________________________________________________________ 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 _______________________________________________________________________
