New Activity for Investigating Anti-SARS Antibodies

The Antibody Engineers NSF ATE project has published its first research project from the January 2022 Hackathon in QUBES.   The project guides students through the process of investigating whether different commercial antibodies are likely to work against SARS-CoV-2 variants.

In the main research component, students use NextStrain.org and GenBank to find protein sequences from new variants and align those sequences to a spike protein complexed with an antibody. Mutations in the antibody binding site are modeled to understand how an amino acid substitution may change the chemical bonds between an antibody and the spike protein.

A spike protein sequence from an Omicron variant was aligned to the spike protein sequence in 7KMG using BLAST in iCn3D.

A YouTube video accompanies the activity and demonstrates how to locate and download the spike protein sequence and carry out the modeling steps with iCn3D. Use the links below to go to QUBES and download the activity.

Porter, S., Hilgert, U., Lannan, E., Stieber, M. (2022). Evaluating the potential for immune escape: how likely is an antibody to protect against a specific SARS-CoV-2 variant?. Antibody Engineering, QUBES Educational Resources. doi:10.25334/82D0-AT65