| 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. References Issue
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1. Luo L., Milon T.I., Tandoh E.K., Galdamez W.J., Chistoserdov A.Y., Yu J., Kern J., Wang Y., Xu W., Development of a TSR-based method for understanding structural relationships of cofactors and local environments in photosystem I, 2025, BMC Bioinformatics, issue 1, vol. 26, DOI 10.1186/s12859-025-06038-y, eissn 14712105 - 2025 - в издания, индексирани в Scopus
2. Miao C., Zhao Q., Zhang Y.-T., Luo S.-Q., Han X., Wen Y., Wu R., Yan Q.-G., Huang X., Wang Y., Zhao S., Lang Y.-F., Zheng Y., Zhao F., Du S., Cao S.-J., RAB4B and Japanese encephalitis virus E protein interaction is essential for viral entry in early endosomes, 2025, International Journal of Biological Macromolecules, issue 0, vol. 306, DOI 10.1016/j.ijbiomac.2025.141452, issn 01418130, eissn 18790003 - 2025 - в издания, индексирани в Scopus
3. Rauniyar K., Milon T.I., Khajouie P., Alabdulkarim R., Chen Y., Kondra S., Raghavan V., Xu W., Development of a Novel Method for Representing 3D Structures of Nucleotides Using the Concept of the TSR Algorithm and Evaluation of the Method Through Studying Specific Interactions Between DNAs and p53, 2025, Proteins Structure Function and Bioinformatics, issue 0, DOI 10.1002/prot.70005, issn 08873585, eissn 10970134 - 2025 - в издания, индексирани в Scopus
4. Kaushik A.S., Agarwal V., Rehman M., Chaudhary R., Srivastava S., Srivastava S., Mahor A., Mishra V., Flavonoids as Modulators of Sirtuin-6 for Management of Metabolic Syndrome: An In Silico Approach, 2025, Biointerface Research in Applied Chemistry, issue 4, vol. 15, DOI 10.33263/BRIAC154.050, eissn 20695837 - 2025 - в издания, индексирани в Scopus
5. Osailan R., Habeeb T., Khalafalla M.A.H., Bashal A.H., Molecular dynamics and electronic structure insights into chloroquine, quercetin, and luteolin binding to HPV-16 E2 protein, 2026, Journal of Steroid Biochemistry and Molecular Biology, issue 0, vol. 256, DOI 10.1016/j.jsbmb.2025.106899, issn 09600760, eissn 18791220 - 2025 - в издания, индексирани в Scopus
6. Rodriguez-Macias J.D., Saurith-Coronell O., Martinez Parra L., Carrascal-Hernandez D.C., Fuentes-Gandara F., Insuasty D., Marquez-Brazon E.A., Integrated In Vitro and In Silico Evaluation of the Antimicrobial and Cytotoxic Potential of Calotropis procera Leaf Ethanolic Extract: From GC-MS Profiling to Molecular Docking and Dynamics, 2025, International Journal of Molecular Sciences, issue 21, vol. 26, DOI 10.3390/ijms262110574, issn 16616596, eissn 14220067 - 2025 - в издания, индексирани в Scopus
7. Zhang L., Xiang C., Zheng N., Kang H., Kong L., Huang W., Peng H., Lian Y., Lu W., Gao M., Wang J., Meksem K., Peng D., Yu F., Liu S., GmSHMT08-Mediated Soybean Cyst Nematode Resistance Is Negatively Modulated by Two Heat Shock Protein 70s in Soybean, 2025, Plant Cell and Environment, issue 0, DOI 10.1111/pce.70296, issn 01407791, eissn 13653040 - 2025 - в издания, индексирани в Scopus
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