COVID-19 AlphaFold2 Models
Model Confidence:
Very high (pLDDT > 90) Confident (90 > pLDDT > 70) Low (70 > pLDDT > 50) Very low (pLDDT < 50) AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions below 50 pLDDT may be unstructured in isolation.
To the right is an AlphaFold2 3D model of the SARS CoV-2 Protein N (UniProt ID: QHD43423) color coded by the pLDDT scores. It corresponds to the highest ranked model in terms of the pLDDT confidence scores, i.e., model 5[1]. At present a number of proteins of the SARS CoV-2 virus have still not been experimentally determined. AlphaFold2 was used to predict 3D models for these proteins using the MIT ColabFold server[1] . For each prediction, five 3D models were predicted, ranked 1 to 5 (with 1 being the best). An example of such a predicted structure is the SARS CoV-2 Protein N (UniProt ID: QHD43423) color coded by the pLDDT scores. Views of these AlphaFold2 predictions can be seen on the following Proteopedia pages:
SARS-CoV-2 protein M - Component of the viral envelope that plays a central role in virus morphogenesis and assembly via its interactions with other viral proteins.[2][3]] SARS-CoV-2 protein N - The primary function of the Nucleocapsid protein (N-protein) is to package the viral genome into a helical ribonucleoprotein (RNP) complex. SARS-CoV-2 protein ORF10 - It is currently unclear whether this region translates into a functional protein.[4][5]]
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