aalphabio/COVID_YM005

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.

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:

@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}
}