RMSD Calculations for Comparing Protein Three-Dimensional Structures

The root Mean Square Deviation (RMSD) is a popular measure of structural similarity between protein structures in the field of bioinformatics. The RMSD calculations involve alignment and optimal superposition between matched pairs of atoms, searching for the lowest RMSD result for both structures. Among the popular methods for calculating the optimal rotation matrix that minimizes the RMSD are the Kabsch algorithm and the Quaternion algorithm. The aim of this research is to present a simple tool for calculation of the RMSD between pairs of aligned three dimensional structures by applying the methods mentioned above. As an implementation language the object-oriented $$C\#$$ programming language has been chosen.