[Dock-fans] building a complex of a protein and SDS micelle

LW wli148 at aucklanduni.ac.nz
Sat Jan 18 00:37:02 PST 2014


Dear dock-fans,
I have a question about building a complex of a protein and SDS micelle. I
have two PDB files, which represent SaposinC(the protein) and SDS micelle.
The structure of SaposinC was solved by NMR in the presence of SDS
micelle.For a reference of the PDB file of SDS micelle, I included a link
for his group below:
http://mackerell.umaryland.edu/MacKerell_Lab.html
Currently I am working on Cp5, which is from the same protein family as
SaposinC, shares similarities in structures and functional characteristics.
What I am planning now on SaposinC, I also plan to do that for Cp5 in
future.
At this moment, I want to do a rigid-body dock on SDS micelle and SaposinC
as the bound structure has been solved by NMR. In the end, I would like to
have a PDB file which represents the complex. I have been looking for
docking tools, but they are either for protein ligand, or protein protein,
or protein DNA, I still am looking for a tool which handles rigid docking
of protein and SDS micelle. Therefore, I am wondering if anyone have any
idea about that?
Many thanks in advance.
Best regards.
Levi
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