Hey there,
I am working on (the theoretical side of) a protein complex whose
structure has been solved. The protein homo-dimerizes, mediated
primarily by two long helices.
Using sequencing alignment and the WHAT IF server, I built monomeric
hybrid models containing the bulk of the known structure and the
dimerization helices of homologous proteins. Naturally, I want to know
how likely they are to form dimers.
To look at the energetics, I've run the phenix geometry regularization
algorithm to minimize clashes and side chain energies. The backbone
conformation only changes minimally. Next I calculated in Rosetta the
energetic scores of the models before and after regularization and
compared with that of the native structure. This gave me some numbers
that are not inconsistent with experiments.
Before I sit down and write this up, I wanted to ask the community if
what I've done makes sense and if there are alternative methods for
minimizing and calculating interface energies. I don't necessarily need
docking algorithms as the interface is known. I just want to get an
energetic description.
Thank you.
Andreas
--
Andreas Förster, Research Associate
Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
