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.