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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?

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/

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

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

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