Frequently Asked Questions

Gowthaman R, Guest JD, Yin R, Adolf-Bryfogle J, Schief WR, Pierce BG. (2020) CoV3D: a database of high resolution coronavirus protein structures. Nucleic Acids Research, In Press. Article PubMed

N-glycans are modeled onto spike glycoprotein structures using a glycan modeling and refinement protocol in Rosetta. This protocol is written using RosettaScripts, and utilizes SimpleGlycosylateMover and GlycanTreeModeler movers for the modeling and refinement.
List of Spike Structures with Modeled Glycans

Contact residues between SARS-CoV-2 spike and mAbs/ACE2 protein complexes were obtained based on the identification of intermolecular all atom residue-residue contacts within a 5Å cut-off.
Visit the spike structures table.

Sequence logos are generated dynamically using the command-line version of WebLogo. A Pan-betacoronavirus multiple sequence alignment and a subset of SARS-like sequence alignment were used as input for generating the sequence logo for user specifed residue range.
Visit the CoV sequence variablity page to generate sequence logo.

The database is updated automatically on a weekly basis, and generally follows the weekly release schedules of the RCSB PDB source.
Visit the Recent Structures table.

We have added the Mol* viewer to the CoV3D site, which shows missing residues as dashed lines in the viewer. The Mol* viewer is linked from the main (NGL) viewer for CoV spike structures.
See the 6VXX Mol* viewer as an example.

Structure alignment output for all pairs of spike chains, which includes residues used in the alignments by the FAST program, is available as a tarball text file on the Downloads page.

We performed hierarchical clustering with a set of 70 non-redundant antibody-RBD complexes (using Manhattan distances) to assign classification to the new antibodies, and we used Canberra distance to identify a closest-matching antibody based on RBD contact profiles. Canberra distance is a measure of distance between two vectors. It is the sum of fraction differences of corresponding values in two vectors. In our contact-based clustering analysis of antibody-RBD complexes, the average intra-class Canberra distance around 20±7, whereas the average inter-class Canberra distance is around 42±12.