ProRMSD Tutorial 1

a tool for automatic atom matching and RMSD calculation

This example will guide a new user through the calculation of the RMSD using ProRMSD.
For this tutorial, we will analyse the "re-docking" results of the cryo-electron microscopy structure of the μOR Opioid Receptor-Gi Protein Complex bound to the agonist peptide DAMGO and nucleotide-free Gi with a resolution of 3.5 Å (PDB code: 6DDF). DAMGO is a flexible opioid peptide, which has multiple rotatable bonds.
The ligand (DAMGO) has been separated from the complex structure of the target (μOR), and then docked back into the target using the docking program HYBRID (OpenEye).
The docking program output is composed of five poses of the ligand.
This file will be used as our input to calculate the RMSD of the predicted poses of the ligand from the known experimental pose in the protein-ligand complex.
  1. Download the input files: click on the two files to download them
  2. Upload these files in the "Upload the structure files" section of the ProRMSD tool
    Click on "Browse..." and select them or drag them in their respective box
  3. Choose the calculation mode: in this tutorial we will calculate the RMSD with the standard algorithm, thus select the "RMSD" button
    If you want to calculate the Backbone RMSD or the Superimposed RMSD click on their respective button
  4. Calculate the RMSD by clicking the "Calculate" button
If the RMSD values are coloured in green, then the job has run correctly.
The output is composed of five different RMSD values, calculated between the reference pose and each one of the predicted poses in the same order as in the input submitted.
> For more information about ProRMSD and how to interpret the results, see ProRMSD Documentation.

ProRMSD

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