I have a predicted secondary structure of a transmembrane protein
containing a really long alpha helix. If I place the secondary structure of
the protein inside membrane (as done for KALP in tutorial) and following
all the steps perform a production MD, is it possible to obtain a
thermodynamically favorable tertiary structure of the same protein ? I mean
generating the folds based on the membrane environment provided.

   Being a beginner in membrane protein simulation, any given advice will
be highly appreciated.

Thank you.

Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

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