aalphabio/COVID_YM005

---
tags:
- chemistry
- biology
pretty_name: Covid RBD Mutagenesis
size_categories:
- 10K<n<100K
---
# Covid mutagenesis dataset (YM_005)

## Overview

YM_005 is a Covid receptor-binding domain (RBD) single-site mutagenesis (SSM) library against a panel of 33 ScFvs.

## Experimental details

We studied the effects of a panel of ScFvs against COVID RBD. In this dataset, our panel of ScFvs are tested in 2 orientations: LH for light-heavy chains and HL heavy-light chains. We explore the local landscape of the RBD in tandem with Covid for epitope mapping by mutating each position. We include a control of ACE2, as the protein of most therapeutic antibodies disrupt.

This dataset includes 62 unique scFvs and 2431 unique RBD sequences.

A more extensive methods section can be found in our publication [here](https://academic.oup.com/abt/article/5/2/130/6584706#372391532).

## Dataset schema

The dataset will contain the following columns:

- `mata_description`: Description of the scfvs; HL/LH indicate orientation of light/heavy or heavy/light
- `mata_sequence`: Scfv sequences
- `matalpha_description`: Description of the RBD mutation
- `matalpha_sequence`: Sequence of the covid binding protein
- `alphaseq_affinity`: Log10 Kd affinity score between the pair of sequences
- `alphaseq_affinity_lower_bound`: Lower bound of affinity
- `alphaseq_affinity_upper_bound`: Upper bound of affinity

## Misc dataset details

We define the following binders:

### A-library (scFvs)
Contains various COVID antibodies. We indicate a few known binders: `ACE2_Full`, `CR3022_scFv_LH_Mod`, `MERS_VHH55`, `SARS_VHH72`, `m396_scFv_LH_Mod`:
We test 2 orientations for binders. If the binder has the "_HL" prefix, it is "heavy-light", and "_LH" is "light-heavy".

### Alpha-library:
Contains the mutation of the RBD in the order of (WT residue, position, mutated residue). Any description with `synWT` is considered a WT replicate.

## Citation
Please cite as follows:
```latex
@article{Engelhart2022,
author = {Emily Engelhart and Randolph Lopez and Ryan Emerson and Charles Lin and Colleen Shikany and Daniel Guion and Mary Kelley and David Younger},
title = {Massively multiplexed affinity characterization of therapeutic antibodies against SARS-CoV-2 variants},
journal = {Antibody Therapeutics},
volume = {5},
number = {2},
pages = {130--137},
year = {2022},
doi = {10.1093/abt/tbac011},
url = {https://academic.oup.com/abt/article/5/2/130/6584706}
}
```