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This interface combines:

The interface can serve simply as a way to obtain neutralization and antibody data for download. We also provide analysis tools to help you analyze the data in various ways.

Data Sources

Neutralization data are taken from publicly-available scientific papers and data repositories. In some cases, these data are in preprint status. In some cases, authors are asked to provide numerical data when their paper contains only non-numerical neutralization data, or to provide clarification on ambiguities. If you have a question about the source of any data, please contact us.

Viral sequence data are taken from GenBank nucleotide or protein databases. Sequences not available in GenBank are constructed based on published mutation lists.

We greatfully acknowledge the Oxford University CoV-AbDab, described by Raybould et al. 2021, as the source of most of the antibody structure links, antibody sequences, and germline data that we include. In accordance with the terms of their open source license, we include the full list of original publications that their data were derived from (in the field named "Germline / structure / sequence sources"). See description of antibody fields below in Antibody details.

Recommended Browsers

CATNAP has been tested in Chrome, Firefox, and Safari. Some functionality may be incomplete in other browsers.

Standardized Names

In order to make CATNAP, we choose a well-known name for each antibody and virus. We try to keep track of the alternative names used in the literature, and record these alternative names as aliases. When you download antibody or virus information from CATNAP, we include the list of known aliases.


Input Selections

The input page allows you to retrieve details about selected Spike sequences and antibodies used in neutralization panels, and to analyze IC50, IC80, and ID50 data.

Select by...

Select Antibodies by...

Select Viruses by...


Retrieve: Antibody details

Select antibodies of interest and retrieve:

Expanded antibody details

After clicking the Expand button, additional antibody details are displayed:

Retrieve: Virus details

Select viruses of interest and retrieve:

Retrieve: Assay

Choose any antibodies and/or viruses and retrieve a downloadable table of available IC50 or other data. When multiple studies assayed the same antibody-virus combination, the geometric mean of the data points is shown (calculated as described below).

Analyze: Assay along with virus sequences
Choose any antibodies, viruses, or study of interest and view neutralization data, displayed together with viral Spike sequences. The resulting Analysis Page is described below.

You can further limit the results of your search using selector boxes.


Analysis Page

The analysis page appears after you choose the "Analyze along with virus sequences" option. Lots of information and further analyses are available.

Analysis page shows 3 aligned windows side-by-side:

Additional information provided under the 3 aligned windows above:


Geometric Means over multiple studies for the same antibody-virus pair

When more than one study assayed the same antibody-virus combination, we present a geometric mean value. A geometric mean indicates the central tendency of a group of n numbers. It is calculated as the nth root of the product of n values. We basically compute means using reported numerical data but when values were reported as a < or > number, we treat them as follows:

Issues Impacting on Geometric Means

The data gathered for the CATNAP tool includes neutralizing antibody data assembled from the scientific literature, as well as sequences from pseudotyped viruses used in neutralizing antibody assays. Inhibitory concentrations IC50 and IC80 (lower values more potent neutralization) are provided for antibodies and their combinations, and inhibitory dilutions ID50 and ID80 (higher values more potent neutralization) for plasma/sera.

CATNAP then provides a geometric mean value for every antibody/Spike pair as a summary value, averaged over all studies that report this combination. Users are able to save CATNAP output, and can download a text file containing all of the independent values and the references that were incorporated into a given geometric mean, and thus get a feel for the content of baseline data.

There are a some important issues to keep in mind as you use these data summaries.

  1. Naturally there is experimental variability between labs and assays, and so the use of a geometric mean is intended to represent an approximate "typical" behavior.
  2. COV CATNAP includes data derived many different types of neutralization assays, including both pseudovirus and live virus assays. We provide the option to limit your results to specific assay types.
  3. If an antibody neutralization curve plateaus very near an IC50 or IC80 cutoff, sometimes it will be just over the cutoff and considered beyond the threshold of a detectable score, while other times it will be just below it. For example, the highest amount of an antibody tested might be 50 ug/ml, and if the IC80 is near 50 ug/ml, sometimes it will be classified as “undetected.” However, if repeated, it may have a detected value just below 50. Depending on the availability of an antibody, and the importance of an experiment, different maximum concentrations can be used for the same antibody in different studies (20, 50, 100, etc.). When we calculate our geometric mean estimate, the default is to exclude values that were beyond the threshold of detection, if any of the repeated experiments were positive. But we also provide an option to calculate geometric mean estimates including tests that were above the threshold, setting a score of “100” for the purpose of the estimation.
  4. Studies often integrate previously-published data sets into their new analysis, and published data tables can include combinations of old and new data. When data points are repeated in the literature, they may be repeated in CATNAP too, as the tool reflects that literature. As a result, not all of the data points that go into the geometric mean calculations are independent, and some data will be over-weighted due to reuse in the literature. Users can, if desired, review the downloaded CATNAP data, pick a subset of papers to minimize this bias, and rerun CATNAP on just those selected papers.

Trim and Re-calculate geometric means

Instead of using the full set of data in CATNAP collection, you can select data from specified papers and calculate geometric means again on those selected ones. This could be useful to reduce data redundancy or to address inconsistencies between studies.


Calculation of N-linked Glycosylation Motifs

Potential N-linked glycosylation sites are highlighted when an N-X-T or N-X-S pattern occurs, where X is any amino acid except proline (P). Any gaps (-) inside the pattern are disregarded.


Calculation of Resistance Relative to D614G

When you check the box "Show resistance relative to D614G" the software will provide an additional output column that calculates and displays IC/ID values relative to D614G. The relative resistance (RR) for D614G is set to "1", and the RR is calculated for the other viruses in the assay by using this formula:

Relative resistance = IC50 for virusX ÷ IC50 for D614G

Example calculation:

virus		IC50		RR
D614G		0.2		1
D614G_A67V	0.4		0.5
WT		<0.01		0.05
Omicron_BA.1	>5		25
Omicron_BA.2	UD		UD

Additional details:

When viewing RR values where a geometric mean has been calculated, you can still view individual values: (1) click the link to "Expand to individual vals", or (2) mouse over any value marked with * and the mouseover will show the study, dataset, and assay type of the individual IC/ID values or individual RR values.



Note: these screenshots were made for the HIV version of CATNAP, but most features are the same for CoV CATNAP.

Input page tips

To SELECT ALL, check the box at the top of the column.

To SORT a column, click the column heading.

To SELECT BY STUDY, click tab.

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Analysis page: Virus information

The viruses analyzed are listed.

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Analysis page: IC50 and IC80 data

Antibodies analyzed are shown. In the example, both IC50 and IC80 data are shown for antibodies 4E10 and b12.

Results are color-coded, as indicated by the scale at upper right.

Asterisks (*) indicate data that are geometric means from multiple studies.

Click "Expand" to see individual data points used to calculate geomeans.

Click Download button to obtain the neutralization data shown, together with virus information.

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Analysis page: Mouseovers

Mouseovers show individual data points used to calculate geomeans. References are also shown.

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Analysis page: alignment

Aligned viral sequences are shown, with the reference sequence at the top.

Numbers 10, 20, 30... are reference sequence coordinates.

When a position has been selected for analysis (see screenshot below), it is highlighted in gray.

Download links provide amino acid or nucleic acid alignments in Fasta or other sequence formats.

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Analysis page: Ab contact positions

Antibody contact positions for the antibodies analyzed are shown, if available.

Click any position and it will appear in the box for "NC_045512 position".

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Analysis page: widen panels

You can slide the width of panels to reveal or hide information.

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Analyze position

Analyze any position in the alignment (for any one antibody) to see additional information:

  • AA Count: amino acids that occur at this position. Count is broken out into the number of viruses detected by the antibody, versus undetected.
  • NxST Count: number of viruses with a predicted glycosylation motif at this residue.
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last modified: Mon Aug 21 16:26 2023

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