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Wednesday, August 18, 2010

How to predict the 3D Structure of known or unknown Protein ?

If you have a nucleotide or amino acid sequence of unknown or known protein and you want to predict its structure then follow the following steps given as :

1.Apply blast to your sequence and get the name of your protein which you are using as a query.

eg your protein name is opsin 1 then go to http://www.ncbi.nlm.nih.gov/ and select structure from search drop down menu and enter the protein name as opsin 1. Then structure of this protein and slight function will be available at this page http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=77531
click the option of download cn3D then download this software for your own system it is a desktop application

it is used to visualize accurately the 3D structure of your protein and you can also rotate your protein with the help of your mouse
The structure will be as

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