I have performed molecular docking with autodock vina for insulin (consists of chain A and B) and a DNA aptamer. I could not analyze the data using pymol following online tutorial, as no interaction are shown between insulin and the DNA aptamer. I tried using Discovery Studio which but I can only select one chain (either chain A or chain B) as ligand, and I could not generate the 2D interaction map. Please give some advice on how to generate 2D interaction map for multichain ligand and/or how to analyze such docking result. Thank you.
Chong Qi : As suggested by Bryan Pandu Permana , you could try YASARA. However, YASARA does not currently have a feature to display a 2D ligand interaction diagram. Nevertheless, in YASARA, you can easily select the chains in the first interacting group and the second interacting group and get an output of the specific interactions at either the residue level or the atomic level. You can also display the interactions in 3D, but not in 2D.
@Rudy J Richardson : you are right. Mostly Yasara and PyMol generate molecule binding site and its interaction in 3D.
@Chong Qi : In my molecular docking thesis, I manually analyzed nearby amino acids of the Protein to Ligand and hydrogen bond using 3D map PyMol and Yasara
If you insist 2D, I searched that it can be done by PoseView
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