I have docked a peptide-protein complex and I want to compare it with another, but as you mentioned my peptide that I docked has a common fragment of known desired binding mode with the peptide that I want to compare it to. I am using pymol to see RMDS. How can I see this desired RMSD in pymol? because aligning the complexes in different ways the RMSD is different... Ty
To compare docking poses, you first superimpose the receptor, the calculate the rmsd between the ligand poses without altering the alignment. I think in PyMOL you can do that with rms_cur (https://pymolwiki.org/index.php/Rms_cur). However, check the manual of your docking program - many of them provide functions to analyze poses by comparing them to a reference pose (e.g. experimental structure or best energy pose) and plot pose energy against rmsd to the reference.
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