I have been using Autodock and discovery studio for my work. I got good results and the binding energies from both the softwares showed similar pattern as expected for all ligands.
I did ligplot analysis for hydrogen and hydrophobic interactions but it was showing difference from the results obtained from discovery studio. One or two amino acid residue showing hydrogen bond with the ligand in ligPlot+ is showing pi - pi interaction in discovery studio.
How can I evaluate the difference?
If this is the only difference then no worry at all. Its not a difference but ligpplot limitation. Ligplot can not work out pi systems thats why you are witnessing the differences.
AUtodock results are not supported in DS visualizer, you can view result of DS and autodock in Pymol viewer.
All the best!
I perfectly agree with Lalit. It is better to analyse the results obtained from DS and AD in pymol viewer as it overcomes the limitation of ligplot and also allows both the results to be treated as same.
Hope it works for you.
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