PDB provides ligand information, but what about the proteins not submitted to PDB, is there any way to get active site information with out using ligand ??????? Please suggests online tools or soft wares which you have come across and got the results. I mean not the website like scibio-iitd, COFACTOR, FINDSITE, Concavity etc.
Hi Kamal,
You can predict the catalytic site for your enzyme if you its PDB code, Uniprot ID or EC number by using Catalytic Site Atlas from EMBL EBI site, here is the link http://www.ebi.ac.uk/thornton-srv/databases/CSA/
I have used it for my enzyme and crystallographic studies revealed the same site. You may give a try.
Good luck
Lokesh
Hi Kamal
We have had good results with Olivier Lichtarge's "Evolutionary Trace" analysis. Never hurts to use as many independent methods as possible. References and server below.
http://mammoth.bcm.tmc.edu/ETserver.html
Hi Kamal,
Enzymes with buried active site are totally unpredictable!
Philippe
Hi Kamal,
If you have done random mutational studies and thus have a number of variants of the same protein and then the measured catalytic efficiency for each variant, then you can use the SigniSite server to perform an automated statistical analysis of residue-to-efficiency association.
http://www.cbs.dtu.dk/services/SigniSite/
http://www.cbs.dtu.dk/services/SigniSite/
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