hello
i did docking by cluspro on my receptor and ligand that both of them have been modeled by modeller according to crystal structure of their template. both of my molecule have up to 30% identity to their crystal structure. but unfortunately after docking when i compare my complex with it's crystal structure complex i found too much rotation of my ligand compare with it's crystal structure.so i want to use software to calculate rotation between my ligand after docking and it's crystall structure. have any software to do this? thanks
Let P1L1 be the (experimental) crystal structure of the protein P1 with bound ligand L1 in the binary complex. Let P2L2 be the binary complex structure where the ligand L2 is docked onto the protein P2 using cluspro. Perform a 3D-superimposition of L1 in P1L1 to L2 in P2L2. With L1 and L2 thus superimposed, take their respective protein parts P1 and P2, then align them (using CE for example). The screen output or the log file generated after the program run should indicate the angle that was used by the program to 3D- superimpose P1 with P2. This is the rotation angle you want.
I suggest to use Docking software such as Autodock, cause Cluspro primarily used for protein-protein interaction.
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