RMSD stands for Root Mean Square Deviation. It is the square root of the average of the squared distance between each mapped pair of point. It is commonly used to measure degree of similarity in protein structure. RMSD is used in 3D
geometry of molecules to measure distance between a given set of points, typically atoms.

This programs fits two molecular structures (drug, protein) and calculates the Root Mean Square Deviation (RMSD) between them giving an idea about their structural similarity. The resultant superimposed structures can be downloaded and viewed in a visualization software like ViewerLite, Rasmol etc.

[Sample File 1] [Sample File 2]

             Input PDB file1 :
              Input PDB file2 :

Instructions for using the Tool

  1. Upload 2 RCSB format PDB files.
  2. Click submit.

Please feel free to send your suggestions and comments at

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