I have used the SwissDock to perform the docking with three different ligands, i would like to calculate the binding energy of each ligand. But I don't know how to calculate it using UCSF Chimera. If anyone know this kindly let me know the procedure.
You can do this using Autodock VINA. Take a look at the instructions on this link:
http://sebastianraschka.com/Articles/2014_autodock_energycomps.html#other-scoring-functions-and-tools
If you insist on using UCSF chimera, have a look at the ViewDock Tutorial:
https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html
If you have used protien as receptor, you can use following online server
http://www.scfbio-iitd.res.in/software/drugdesign/bappl.jsp
or if the receptor is DNA you can use this server (link given below)
http://www.scfbio-iitd.res.in/software/drugdesign/preddicta.jsp
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