ADL: Is lipid membrane building and SASA useful for docking studies

Kalyan chaitanya kalyanpulipaka at gmail.com
Tue Jan 1 09:37:22 PST 2008


Dear all,

I am working on Transmembrane protein (TMP), i have a homology model of TMP,
now I am interested in understanding the binding interactions of TMP with
its ligand (which is a polypeptide [32 amino acids]), in due course i
studied couple of papers where they have build and lipid membrane and did
molecular dynamics,

*My questions are-*

   1. i am not aware if the polypeptide have any interactions with lipid
   membrane surface, but building a lipid membrane and then performing MD and
   Docking would be a right way of doing ?
   2. how important it ld be to study Solvent accessible surface of TMP,
   before and after Docking?
   3. can any one suggest any good reliable Active site Prediction
   Servers?

Please throw some light on these queries

Thank you in advance,

Regards,
Kalyan


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