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Putative ligand binding site formed by dimer.

protein docking dimer

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#1 JBB2412

JBB2412

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Posted 29 May 2014 - 08:09 PM

I have a protein that forms a dimer and the dimer has a groove that we hypothesize is used for binding a ligand or small molecule. I want to run the structure through a database to see if it get's any hits but everything I've found that accepts .pdb files won't accept the protein as the dimer >500 sequences (750) and everything that accepts the FASTA sequence doesn't have an option to enter both sequences to check against the dimer.

I need some sort of idea as to what will bind so I can narrow down my criteria and start some in-vitro binding assays.

Any and all suggestions would be greatly appreciated.

Here's the link to the .pdb of the protein if that helps.

http://www.rcsb.org/...tructureId=4MDU

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  • asm070_dimer_surface_front_black.png






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