COVID-19 AlphaFold2 Models: Difference between revisions
No edit summary |
No edit summary |
||
| Line 7: | Line 7: | ||
'''[[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="MIT_ColabFold"/><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="Zhang_Lab"/><ref name="Zhang"/>. | '''[[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="MIT_ColabFold"/><ref name="Zhang_Lab"/><ref name="Zhang"/>. | ||
'''[[SARS-CoV-2 protein NSP6]]''' - Plays a role in the initial induction of autophagosomes from host reticulum endoplasmic | '''[[SARS-CoV-2 protein NSP6]]''' - Plays a role in the initial induction of autophagosomes from host reticulum endoplasmic<ref name="MIT_ColabFold"/><ref name="Zhang_Lab"/><ref name="Zhang"/>. | ||
'''[[SARS-CoV-2 protein ORF10]]''' - It is currently unclear whether this region translates into a functional protein | '''[[SARS-CoV-2 protein ORF10]]''' - It is currently unclear whether this region translates into a functional protein<ref name="MIT_ColabFold"/><ref name="Zhang_Lab"/><ref name="Zhang"/>. | ||
</StructureSection> | </StructureSection> | ||
== References == | == References == | ||
<references/> | <references/> | ||
Revision as of 00:18, 8 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. As an example, 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], which was developed by Sergey Ovchinnikov, Milot Mirdita and Martin Steinegger. At present, there a still a number of proteins from the SARS CoV-2 virus whose 3D structures have not yet been experimentally determined. AlphaFold2 was used to predict these structures using the MIT ColabFold server[1]. For each prediction, five 3D models were predicted, ranked from 1 to 5 (with 1 being the best). Views of these AlphaFold2 predictions can be seen on the 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[1][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[1][4][3]. SARS-CoV-2 protein NSP6 - Plays a role in the initial induction of autophagosomes from host reticulum endoplasmic[1][4][3]. SARS-CoV-2 protein ORF10 - It is currently unclear whether this region translates into a functional protein[1][4][3]. |
| |||||||||||
ReferencesReferences
- ↑ 1.0 1.1 1.2 1.3 1.4 1.5 MIT ColabFold
- ↑ Modeling of the SARS-COV-2 Genome
- ↑ 3.0 3.1 3.2 3.3 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
- ↑ 4.0 4.1 4.2 Cite error: Invalid
<ref>tag; no text was provided for refs namedZhang_Lab