Description of a newly solved structure

From: sadaf iqbal
Date: 1 December 2011 04:49

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

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From: Sean Seaver


Hi Sadaf,

I would start with BRENDA ( http://www.brenda-enzymes.org/ ) for an overview on the protease.  The web servers and databases that you should consider will be highly dependent on the details of your particular structure.  I put together a list of some programs/servers/databases that you may want to consider ( http://bit.ly/d2I11n ).  I hope it helps.

Take Care,

Sean Seaver

P212121
http://store.p212121.com/

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From: Katherine Sippel

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

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From: Nadir T. Mrabet

I would also suggest using MolProbity to assess structure quality.

Best,

Nadir