For drawing a 2D fold topology I'd suggest TopDraw ( http://www.ccp4.ac.uk/html/topdraw.html). To see if you structure looks like other structures I'd look at the DALI server ( http://ekhidna.biocenter.helsinki.fi/dali_server/). Dali is pretty good for digging out results/discussion fodder because it gives you another structure(s) to compare. PISA would be my suggestion for roughly identifying any oligimerization though it's best to back those claims up with experimental data. If you've got ligands bound Gerard Kleywegt and the PDBe staff have put together a lovely means of searching and representing motifs which is also useful for comparative purposes ( http://www.ebi.ac.uk/pdbe-site/pdbemotif/). There are a panoply of good figure generating softwares available but my personal preference is Pymol for it's flexibility, comprehensive wiki, and supportive users groups ( http://www.pymol.org/).
If your just looking for a description of what to put into a results and discussion section for a new structure you might try browsing through the Acta Cryst D archives for some good examples. Hope this helps, Katherine On Wed, Nov 30, 2011 at 10:49 PM, sadaf iqbal <[email protected]>wrote: > Hello everyone, > > I have submitted one cysteine protease structure in PDB and now i have to > describe the structure completely for my PhD thesis. I know some web > servers who are good to provide knowledge about protein but i would like to > ask expert persons of this field as i am quite new in describing a > structure. Which softwares/web servers you prefer when you are going to > describe one complete native structure? I am a chemist basically. > > Thanks in advance > > Sadaf Iqbal > PhD Scholar > ICCBS, University of Karachi, Pakistan. > & Visiting Scientist > University of Hamburg, Germany. >
