Predictions of the SARS-CoV-2 Omicron (B.1.1.529) Variant Spike Protein Receptor Binding Domain Structure and Neutralizing Antibody Interactions.

Colby T. Ford, Ph.D., Denis Jacob Machado, Ph.D., and Daniel A. Janies, Ph.D.
The University of North Carolina at Charlotte

Companion repository for the following articles:

• Frontiers in Virology Article: https://www.frontiersin.org/articles/10.3389/fviro.2022.830202

• Medium posts:
  • Protein Structure Prediction of the new B.1.1.529 SARS-CoV-2 Spike Variant with AlphaFold2
  • Predicted Protein Interactions of the SARS-CoV-2 B.1.1.529 Variant with Neutralizing Antibodies
  • Quick Note: What’s up with the new SARS-CoV-2 BA.2.75 and BA.5 variants?

YouTube Video:

Media:

This work was also mentioned in:

• WIRED: https://www.wired.com/story/ai-software-nearly-predicted-omicrons-tricky-structure/
• The Economist: https://www.economist.com./briefing/2021/12/04/omicron-looks-ominous-how-bad-is-it-likely-to-be
• Fortune: https://fortune.com/2022/01/12/biontech-instadeep-ai-early-warning-covid-19-variants-of-concern-omicron-delta/
• Syfi Technologies: https://www.sify.com/movies/omicron-may-not-completely-evade-vax-immune-response-us-study-news-bollywood-vmjm5tgabahbj.html
• Medical News: https://www.news-medical.net/news/20211208/AlphaFold-AI-predicts-SARS-CoV-2-omicron-variant-might-not-evade-antibody-neutralization.aspx
• Precision Vaccinations: https://www.precisionvaccinations.com/2021/12/07/predicting-sars-cov-2-omicron-variant-impact-ai
• The Print: https://theprint.in/health/omicron-unlikely-to-completely-evade-antibodies-us-study-using-ai-tool-suggests/778403/
• ChemDiv: https://www.chemdiv.com/company/media/pharma-news/2022/free-ai-protein-software-packages-nearly-predicted-structure-of-the-omicron-coronavirus-variant-corr/
• Latest Game Storage: https://latestgamestories.com/2022/01/10/this-ai-has-almost-exactly-detailed-the-structure-and-operation-of-omicron/
• SiaSat: https://www.siasat.com/omicron-may-not-completely-evade-vax-immune-response-us-study-2238739/

Resources:

Omicron (B.1.1.529) Info:

• B.1.1.529 Sequence (from GISAID) and Wuhan Reference Sequence: /sequences
• List of B.1.1.529 Spike mutations: B.1.1.528_Spike_Mutations.xlsx

Receptor Binding Domain Structure:

• AlphaFold2 Code: AlphaFold2.ipynb
• Predicted B.1.1.529 Spike receptor binding domain PDB structure: SARSCov2_B11529_Srbd_80403_relaxed_model_1_rank_1.pdb
• Actual Cryo-EM Structure from Mannar et al. 2021: https://www.rcsb.org/structure/7T9J

Protein Interactions:

AlphaFold2 Omicron Structure Docking:

• Predicted interaction PDB for B.1.1.529 with C105 antibody: 6xcm_Fab_pred_docking_cluster1_1.pdb
• Predicted interaction PDB for B.1.1.529 with CC12.1 antibody: 6xc2_Fab_pred_docking_cluster1_1.pdb
• Predicted interaction PDB for B.1.1.529 with CC12.3 antibody: 6xc7_Fab_pred_docking_cluster1_1.pdb
• Predicted interaction PDB for B.1.1.529 with CV30 antibody: 6xe1_Fab_pred_docking_cluster1_1.pdb

RoseTTAFold Omicron Structure Docking:

• Predicted interaction PDB for B.1.1.529 with C105 antibody: 6xcm_Fab_RFpred_docking_cluster2_1.pdb
• Predicted interaction PDB for B.1.1.529 with CC12.1 antibody: 6xc2_Fab_RFpred_docking_cluster3_1.pdb
• Predicted interaction PDB for B.1.1.529 with CC12.3 antibody: 6xc7_Fab_RFpred_docking_cluster3_1.pdb
• Predicted interaction PDB for B.1.1.529 with CV30 antibody: 6xe1_Fab_RFpred_docking_cluster1_1.pdb

Subvariants

• BA.1: subvariants/BA.1
• BA.2: subvariants/BA.2
• BA.2.75: subvariants/BA.2.75
• BA.5: subvariants/BA.5