Hi everybody,
This is a general question regarding the applicability of MMPBSA for a particular problem which I summarise below.
I'm dealing with a number of related crystallographic models whose biological unit is in dimeric form. The monomers are in the range of 125-140 residues.
The area of the dimer interface is small and not well conserved. This has led to the suggestion that dimerisation is an artifact of the crystallisation process. On the other hand biochemical experiments have established the existence of dimers under particular conditions.
My question is the following. Is it legitimate to treat chainA as the receptor, chainB as the ligand, the dimer as the complex and subject them to MD followed by the use of MMPBSA.py to derive Gibbs free energies of binding? Are there any caveats in using such an approach.
Many thanks
George
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Received on Sat May 28 2011 - 02:30:02 PDT
