10.25394/PGS.12245843.v1 Xusi Han Xusi Han Computational Methods for Protein Structure Comparison and Analysis Purdue University Graduate School 2020 protein structure cryo-EM X-ray crystallography 3D Zernike Descriptors Fast Fourier transform (FFT) Protein Shape structure alignment Atomic Structure electron density map Computational Biology Structural Biology Biophysics 2020-05-05 01:27:24 Thesis https://hammer.purdue.edu/articles/thesis/Computational_Methods_for_Protein_Structure_Comparison_and_Analysis/12245843 Proteins are involved in almost all functions in a living cell, and functions of proteins are realized by their tertiary structures. Protein three-dimensional structures can be solved by multiple experimental methods, but computational approaches serve as an important complement to experimental methods for comparing and analyzing protein structures. Protein structure comparison allows the transfer of knowledge about known proteins to a novel protein and plays an important role in function prediction. Obtaining a global perspective of the variety and distribution of protein structures also lays a foundation for our understanding of the building principle of protein structures. This dissertation introduces our computational method to compare protein 3D structures and presents a novel mapping of protein shapes that represents the variety and the similarities of 3D shapes of proteins and their assemblies. The methods developed in this work can be applied to obtain new biological insights into protein atomic structures and electron density maps.