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Sandeep Kaur, Neblina Sikta, Andrea Schafferhans, Nicola Bordin, Mark J. Cowley, David M. Thomas, Mandy L. Ballinger, Seán I. O’Donoghue (UNSW)
In this work, we extended Aquaria - a powerful 3D protein structure visualisation tool - to enable a user to specify variants and find matchings structures containing these variants. Using our resource we enumerated all experimental structures containing variants founds in SARS-CoV-2’s spike protein from the omicron lineage, and found a structure deposited in PDB prior to Omicrons emergence - containing two variants, namely N501Y and Q498R, now observed in omicron. The authors depositing this structure found that the presence of these two variants increased binding of spike with ACE2 by 1000 fold - due to the formation of π-π stacking between this variant Y in spike and this Y in human ACE2. This may explain Omicrons increased transmissibility.