Hello Vijay,

Check the following:

Pockets: http://sts.bioengr.uic.edu/castp/  (Castp server)

Protein functional sites:

Qsite: http://www.bioinformatics.leeds.ac.uk/qsitefinder/

SARIG: http://bioinfo2.weizmann.ac.il/~pietro/SARIG/V3/index.html

THEMATICS from Mary Jo Ondrechen at Northeastern University is very good. Unfortunately, there is no web server as of yet that I am aware off. However, they are very helpful. If you have a structure of interest
you can write to her and ask them to run it through their program.

In all the above methods the only necessary input is the structure of the protein in PDB format. Thus, they are very good when you have novel or orphan (no homology to others) structures . There are several methods that rely on comparison with known structures. You can check:

http://wikiomics.org/wiki/Searching_for_3D_functional_sites_in_a_protein_structure

for a summary.

Hope this helps.

Maurizzio

At 07:12 AM 7/18/2006, you wrote:
hello,

Can anyone pl tell me programs which can find the protein surface properties such as pockets, different potential surfaces and active sites.
thanks in advance.

Regards,
vijay


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