Dear all,
I am trying to estimate binding affinity between a small peptide (consisting of a dozen of amino acids) and DMPC lipid bilayer. My calculation attempts were always terminated at the normal mode analysis. I have searched but failed to find information about such calculation done by others.
Has anyone successfully done the MMPBSA for system with membrane or can anyone, please, tell me if it is possible to do so currently?
Any answers or comments will be highly appreciated
Dear Huy Dinh Quoc Pham ,
You might have a look at the following:
https://www.researchgate.net/post/Regarding_MMPBSA_MMGBSA_Calculations
Beside the approach you use I suggest that you have look at Heliquest. This is a program that predicts lipid binding potential. The use of the so-called Heliquest based Eisenberg plot approach allow you to say a lot about the lipid binding potential of your peptide:
Article New User-Friendly Approach to Obtain an Eisenberg Plot and I...
Additionally, you could consider MCPep, a nice and user-friendly program to study peptide-lipid interactions in silico:
http://bental.tau.ac.il/MCPep/
PS. Unfortunately this program is down for now due to some technical problems but have a look at for example:
Article Identification and in silico analysis of helical lipid bindi...
Article The role and significance of potential lipid-binding regions...
To see what you can achieve with both mentioned approaches. See for example:
Article Identification of Possible Lipid Binding Regions in Food Pro...
Best regards.
I have this same question, if it is possible to use the MMPBSA method to quantify the membrane-peptide interactions ?
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