Hi to all, I'have to perform a docking in haddock. i have determined the most susceptible residues upon ligand binding by chemical shift perturbation. now i need to determine which among the are active resiues, and i need to calculate which of them have a >=50% solvent accessibility.
I know that NACCESS is a very reliable program to do that, but i have to send a mail (a normal mail) to get the code for decrypt the rar file.
Is there anyone that could give me that code? or is there any software as reliable as NACCESS capable of perform that calculations?
Thank u
Hi Antonio,
You may want to take a look at the surf and molsurf commands in AmberTool's cpptraj program. Also, Ken Dill's group recently released Triforce (http://dillgroup.io/). I haven't used it myself yet though.
Pawel
Hello Antonio,
what do you mean with "i have to send a mail (a normal mail) to get the code for decrypt the rar file"?
As an alternative you can try POPS (http://mathbio.nimr.mrc.ac.uk/wiki/POPS)
u can use tool GMXPBSA, which is free tool...
Discovery studio 4.1 module
QM/MM binding energy calculation can also be used to predict SASA..
PDBe PISA server : http://www.ebi.ac.uk/pdbe/pisa/
CASTp : http://sts.bioe.uic.edu/castp/
You can use my software online POPS for single molecules and POPSCOMP for complexes
http://mathbio.nimr.mrc.ac.uk/wiki/POPS
http://mathbio.nimr.mrc.ac.uk/wiki/POPSCOMP
exmples files are online
ff
Hi Antonio,
We used GETAREA to calculate the SASA for our protein-protein docking study also using HADDOCK.
http://curie.utmb.edu/getarea.html
You can also take a look at our study for ideas:
http://dx.doi.org/10.1371/journal.pone.0062996
Best regards,
Chanin
Maybe a bit late, but I've written an open source package for this: https://github.com/mittinatten/freesasa
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