I would also suggest using MolProbity to assess structure quality.
Best,
Nadir
Pr. Nadir T. Mrabet
Structural& Molecular Biochemistry
Nutrigenex - INSERM U-954
Nancy University, School of Medicine
9, Avenue de la Foret de Haye, BP 184
54505 Vandoeuvre-les-Nancy Cedex
France
Phone: +33 (0)3.83.68.32.73
Fax: +33 (0)3.83.68.32.79
E-mail: Nadir.Mrabet<at> medecine.uhp-nancy.fr
On 01/12/2011 16:34, Katherine Sippel wrote:
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 <sadaf_che...@yahoo.com
<mailto:sadaf_che...@yahoo.com>> 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.
