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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