SpikeScape: A Tool for Analyzing Structural Diversity in Experimental Structures of the SARS-CoV-2 Spike Glycoprotein

In this application note, we describe a tool which we developed to help structural biologists who study the SARS-CoV-2 spike glycoprotein. There are more than 500 structures of this protein available in the Protein Data Bank. These structures are available in different flavors: wild type spike, different variants, 2P substitutions, structures with bound antibodies, structures with Receptor Binding Domains (RBD) in closed or open conformation, etc. Understanding differences between these structures could provide insight into how the spike structure changes in different variants or upon interaction with different molecules such as receptors or antibodies. However, inconsistencies among deposited structures, such as different chain or sequence numbering, hamper a straightforward comparison of all structures. The tool described in this note fixes those chain inconsistencies and calculates the distribution of the requested distance between any two atoms across all SARS-CoV-2 spike structures available in the Protein Data Bank (excluding PDB files with only spike fragments such as the RBD), with the option to filter by various selections. The tool provides a histogram and cumulative frequency of the calculated distribution, as the ability to download the results and corresponding PDB IDs.