[Chimera-users] dock

LW wli148 at aucklanduni.ac.nz
Mon Apr 22 18:53:05 PDT 2013


Dear all,
As attached, I have a structure of Saposin C in the presence of SDS micelle
solved using NMR. I took the first model out of its 20-structure ensemble
and generated SapC_one_model.pdb. I also have a PDB file(as attached )built
to model SDS micelle surrounded by water. Does Chimera allow people to dock
these two molecules and generate a combined PDB file for further analysis?
While the structure of Saposin C in the presence of SDS micelle, NMR data
indicate that the open hydrophobic core is in contact with SDS micelle. Is
it possible to use Chimera to determine the relative orientation of the two
molecules where (i), they are in intimate contact, (ii), there is no clash,
(iii), the shape complementarity is at its optimal?
Any clue would be much appreciated.
Levi
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