SELECTION OF PROTEIN CRYSTAL (PDB) STRUCTURE FOR DOCKING

HOW TO SELECT  A PDB FILE FOR DOCKING

Selection of  proein structure form RCSB protein data bank is an important step in molecular docking process.There are more than  76003 Structures are available ,you can download the protein structure of your interest from the website http://www.rcsb.org/pdb/home/home.do .first you have to check whether the 3D structure of the corresponding target has been deposited or not ,if not the 3D structure of the target protein is constructed through homology modelling.While selecting any structure from PDB the following things should  keep in mind .

1. The structure available is a co crystallized with a drug , which is the appropriate starting process for the docking.
2. If the structure of the protein doesnt contain a native ligand (drug),then the binding site has to be identified wih appropriate software (blind docking using autodock will work) then docking has to be progressed with
3. Co-relation of  docking results will be good if  protein structure source and expression is Homo sapiens
4. Take those protein structures which are having resolution less than 2.5 angstrom.
5. The R value should be as close to zero.
6. The  R free value should be close to R value.  

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