Is there a source where I can find the 3D structures of the different protein alleles?

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Zahid Khan

take the sequence of your protein and do a BLAST on uniprot database selecting a PDB data base .

If 3D structures for different variants are not available , you can build these structures very easily by homology modelling

Nawroz Abdulrazzak

Below is the link of 10 Free Software for protein 3D structure visualization.I think this may solve your problem.

http://www.bioinformatics-made-simp...0-free-software-for-protein-3d.html

10 Free Software for protein 3D structure visualization~ Bioinformatics Made Simple.com

10 Free Software for protein 3D structure visualization