Tool for prediciting Lipid binding domain in a given protein

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crisspy
crisspy's picture
Tool for prediciting Lipid binding domain in a given protein

Dear Friends,

Is there a way/tool available on net to predict lipid binding domain(s) in a given protein??

I have tried several available tools on NCBI and SMART search but nothing was helpful.

If someone knows a particular tool/search engine that I can use for predicting Lipid binding domain in protein of my interest then please post the website address....

Thanks for reading this post.

Crisspy

sichan
sichan's picture
Hi Crisspy,

Hi Crisspy,
This group used support vector machines to predit lipid binding protein domains.  The software can be accessed here: http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi
The associated paper is located here:
http://www.jlr.org/cgi/content/full/47/4/824
 
Good luck and let us know how it works out!
 

sichan
sichan's picture
A quick google/pubmed search

A quick google/pubmed search showed that these same authors also used SVMs to predict metal-binding proteins.  Check out this BMC Bioinformatics paper and its associated references:

http://www.biomedcentral.com/1471-2105/7/S5/S13
 
In case there are other domains you may be interested... :-)

Ash ahmad
Ash ahmad's picture
Lipid binding

My protein is MCR1, a transferase and is known to modify Lipid A. I tried SVM server, and it says no entry found. Any other suggestions?I read Scott et al paper, but the algorithum they have explained is not very clear to me, how to apply it in real sense. Regards,