GitHub Repository
Created On
Updated On
The RMSD measures the average distance between atoms of 2 protein or ligand structures. By default, all atoms but hydrogen atoms of the protein are included in the RMSD calculation.

More details

Use Cases Limitations Evidence Owner's Insight

This app computes the root mean square deviation (RMSD) in Angstrom between two PDB-format structures. It is important to note that both PDB files must have an identical number of atoms for the script to function properly. The RMSD quantifies the average distance between corresponding atoms in two protein or ligand structures using the RMSD equation. Typically, RMSD calculations exclude hydrogen atoms, focusing on C-alpha or main-chain atoms in proteins.

Both structures must contain the same number of atoms in similar order.

Based on the GitHub:

Try out with this data:


Warning: App may appear to work well but has not been peer reviewed. Not intended for clinical use. Use with caution.

  • Favorites: 1
  • Executions: 25

  • Drug Discovery & Development


Kinal Patel

Member since