The article introduces Bio3d, an R package designed for the comparative analysis of protein structures. The package facilitates the characterization of internal conformational differences and inter-conformer relationships, providing a framework for understanding protein structural evolution. Key features include automated structural superposition, principal component analysis (PCA), and various tools for processing and exploring structure and sequence data. The method is particularly useful for analyzing multi-domain proteins and molecular motors, as demonstrated through examples such as kinesin. The bio3d package is freely available under a GPL2 license, offering a robust tool for researchers in structural bioinformatics. The authors highlight the agreement between their automated results and those established by human experts, emphasizing the package's potential in identifying common structural and dynamic features in diverse protein families.The article introduces Bio3d, an R package designed for the comparative analysis of protein structures. The package facilitates the characterization of internal conformational differences and inter-conformer relationships, providing a framework for understanding protein structural evolution. Key features include automated structural superposition, principal component analysis (PCA), and various tools for processing and exploring structure and sequence data. The method is particularly useful for analyzing multi-domain proteins and molecular motors, as demonstrated through examples such as kinesin. The bio3d package is freely available under a GPL2 license, offering a robust tool for researchers in structural bioinformatics. The authors highlight the agreement between their automated results and those established by human experts, emphasizing the package's potential in identifying common structural and dynamic features in diverse protein families.