I performed docking of two molecules (one protein molecule and other one is its inhibitor) by using Hex software and saved the docked molecules. But when i am analyzing the same file in pymol and swisspdbviewer, both molecules are showing interaction via Pymol while they are not showing any interaction when i am using swisspdbviewer for visualization. How is it possible that the same file is showing different structures in different visualization software?
Every software has its own criteria to make/show hydrogen bonds.
For instance look into the default values in pymol which will be different from spdbv.
In pymol, we reflect the interactions as putative since its not reflecting the free energy of binding predicted by AutoDock.
It is better to use ADT to analyze interactions.
every software has its own principle of working and interaction analysis. You can use Chimera and VMD too for post docking analysis.
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