Hello all of you scientists,
I really have no business using bioinfomatics software, but suffice to say, I have to.
What I´m currently trying to do is perform a test of Gramm, the bare-bones protein docking program. In order to perform a test of the program, I figured that I would see if would properly predict the self-assembly configuration of alpha and beta tubulin. That started to look complicated, so then I discovered that bacteria have a similar protein called FtsZ which self assembles into little filaments.
Looking all of this up on the RCSB database, I found that all of the PDB files had all of the proteins somehow combined with other proteins. They simply didn´t have the proteins by themselves.
Is there a place to find a PDB file with these proteins in isolation? Am I doing the wrong query? Does my question not make sense? Is there another simple protein that self assembles I could use for this test?
Any ideas?
-Todd
