I want to do a docking study with a lipid membrane and a peptide. Peptides are usually short, 5-50 amino acid. Do you know a tool or server I can use for this aim?
SDA & webSDA (Simulation of Diffusional Association)
https://mcm.h-its.org/sda7/doc/doc_sda7/index.html
http://mcm.h-its.org/webSDA
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i have no personal experience with this technique.
Docking of peptides like that is incredibly difficult - the peptides tend to curl up on themselves, which is obviously the wrong solution. Even a 4-5mer tends to give quite unreasonable results with even many commercially available packages. You might have better luck with molecular dynamics, like Gromacs, but that's also a much more intensive calculation.
Thanks to all answers.
Dear William, I use molecular dynamic methods for this but my aim is to save time and computer power when I use namd or gromacs, because sometimes peptide spends a lot of time in the solvent and it takes time to interact with the membrane.
Dear Suleyman,
The follow webserver could be helpfull http://opm.phar.umich.edu/server.php altought it is designed to orientate proteins into lipid membranes not for peptides, once you find the proper orientation it´s possible that conduct a short time clasic molecular dynamics simulation employing NAMD, GROMACS or AMBER with the proper force field but I also think that other option could be that you find or build a short lipid membrane and dock them with ClusPro but again, this webserver is aimed to dock protein-protein.
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