Spike Features Help

The Spike Features search interface provides the coordinates of known antibody contact sites and antibody-related features. The data from this database are also displayed on the analysis page of the COV CATNAP neutralization database. These sites are often associated with antibody-driven escape.

MAb name

The commonly-used name of the monoclonal antibody.

Reference

The reference(s) from which the information was obtained. There may be other references that have been important in elucidating the antibody or feature, but we only list the reference from which we obtained the data shown.

Feature Type

The type of site:

• binding - sites associated with (or altering) the binding of an antibody; often defined by alanine scanning or other mutational approaches.
• contacts - the contact residues of the antibody; usually defined by X-ray crystallography or cryo-EM.
• neutralization - sites associated with (or altering) the neutralization of an antibody; often defined by alanine scanning or other mutational approaches.

Method

The experimental method(s) used to define the feature.

Binding Type

Search for mAbs by the protein that the mAb binds to. The protein name includes the RBD binding class, if known. Binding classes are as defined by Barnes et al. 2020 PMID 33045718. The class given is typically taken from subsequent publications specific that the mAb.

Epitope Group

Search for Abs by their epitope group. Epitope groups are as defined by Cao et al. 2022 PMID 35016194.

Spike AA position

The coordinate of the amino acid where the contact or feature occurs. The coordinates are numbered based on the Spike Wuhan-Hu-1 reference sequence (GenBank NC_045512).

Input allows searching for a single amino acid position, or multiple comma-separated values, for example: 312,313,314,410

Text search on Annotation

Free input text that will search the annotation text. For example, a search for "hydrogen" will find features involving hydrogen bonds.

Feature ID

An arbitrary database ID for each feature.

Initial search results will show a list of features matching the search criteria. Clicking on Details will show the following:

Position

A list of the positions for this feature.

NC_045512 AA

The amino acid at this position in the Spike reference sequence.

Annotation

Descriptive information about the feature. For example, the description for neutralization features will normally state whether a particular mutation increases or decreases neutralization.

Spike Features search interface

COV CATNAP search interface

Downloads for COV CATNAP and Spike Feature databases