COVID-19 AlphaFold2 Models: Difference between revisions
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[[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<ref name="Zhang Lab"> [https://zhanglab.ccmb.med.umich.edu/COVID-19/ Modeling of the SARS-COV-2 Genome]</ref><ref name="Zhang"> pmid 32200634</ref>. | [[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<ref name="Zhang Lab"> [https://zhanglab.ccmb.med.umich.edu/COVID-19/ Modeling of the SARS-COV-2 Genome]</ref><ref name="Zhang"> pmid 32200634</ref>. | ||
[[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<ref name=" | [[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<ref name="Zhang_Lab"><ref name="Zhang">. | ||
[[SARS-CoV-2 protein ORF10]] - It is currently unclear whether this region translates into a functional protein.<ref name="Zhang_Lab"><ref>pmid 32200634</ref>] | [[SARS-CoV-2 protein ORF10]] - It is currently unclear whether this region translates into a functional protein.<ref name="Zhang_Lab"><ref>pmid 32200634</ref>] | ||
Revision as of 18:04, 4 February 2022
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) complexCite error: Closing
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ReferencesReferences
- ↑ 1.0 1.1 MIT ColabFold https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb
- ↑ Modeling of the SARS-COV-2 Genome
- ↑ Zhang C, Zheng W, Huang X, Bell EW, Zhou X, Zhang Y. Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1. J Proteome Res. 2020 Apr 3;19(4):1351-1360. doi: 10.1021/acs.jproteome.0c00129., Epub 2020 Mar 24. PMID:32200634 doi:http://dx.doi.org/10.1021/acs.jproteome.0c00129