Autors: Fatima Sapundzhi., Metodi Popstoilov., Lazarova, M. D.
Title: RMSD Calculations for Comparing Protein Three-Dimensional Structures
Keywords: computer modelling, Root Mean Square Deviation (RMSD)

Abstract: 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.



    Numerical methods and applications, 10th International Conference, NMA 2022 Borovets, Bulgaria, August 22–26, 2022 Proceedings, vol. LNCS 13858, pp. 279--288, 2023, Switzerland, Spinger Nature Switzerland AG 2023, ISBN ISBN 978-3-031-32411-6

    Copyright Springer Nature Switzerland AG 2023

    Вид: публикация в международен форум, публикация в реферирано издание, индексирана в Scopus