COVID-19 AlphaFold2 Models: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Joel L. Sussman

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-<StructureSection load='' size='350' side='right' scene='84/842060/Sars-cov-2_protein_n/1' caption='SARS-CoV-2 Protein N'>
+[[Image:SARS-Cov-2-genome.jpg|1000px|center|thumb|SARS-CoV-2 Protein Organization, from Gordon
-{{Theoretical_model}}
+et al. & Krogan (2020)<ref>PMID: 32353859 </ref> )]]
-{{Template:ModelConfidence}}
+[[Image:VirusImage.jpg|left|330px|thumb|Organization of SARS-CoV-2 virus (from Holmes & Enjuanes (2003)<ref>pmid 12775826</ref>)]]
-As an example, to the right, is an '''[[AlphaFold]]2''' 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<ref name="MIT_ColabFold"> MIT ColabFold https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb </ref>.
+==Background==
+At present, there are still a number of proteins from the SARS CoV-2 virus whose 3D structures have not yet been experimentally determined. [[AlphaFold]]2 was used to predict these structures using the MIT ColabFold server<ref name="MIT_ColabFold">[https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb  MIT ColabFold]</ref>, which was developed by [http://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb Sergey Ovchinnikov, Milot Mirdita and Martin Steinegger]. 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:<br>
+==AlphaFold2 Predicted Structures==
+{{Template:COVID Validation}}
+'''[[SARS-CoV-2 protein NSP6]]''' - '''''AlphaFold2 Theoretical Model''''' - Plays a role in the initial induction of autophagosomes from host reticulum endoplasmic<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>.
-At present, there a still a number of proteins from the SARS CoV-2 virus whose 3D structures have not yet been experimentally determined. [[AlphaFold]]2 was used to predict these structures using the MIT ColabFold server<ref name="MIT_ColabFold"> MIT ColabFold https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb </ref>. 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:<br>
+'''[[SARS-CoV-2_protein_NSP11]]''' - '''''AlphaFold2 Theoretical Model''''' - is the 13 amino acid peptide at the C-term of the large SARS-CoV-2 polyprotein ORF1ab (pp1a). Neither its functions, nor if it is expressed ''in vivo'' is clear<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 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"> Modeling of the SARS-COV-2 Genome https://zhanglab.ccmb.med.umich.edu/COVID-19/</ref><ref name="Zhang"> pmid 32200634</ref>.
+'''[[SARS-CoV-2 protein M]]''' - '''''AlphaFold2 Theoretical Model''''' - 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_ORF6]]''' - '''''AlphaFold2 Theoretical Model''''' : Could be a determinant of virus virulence<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 ORF10]]''' - It is currently unclear whether this region translates into a functional protein.<ref name="Zhang_Lab"/><ref name="Zhang"/>.
+'''[[SARS-CoV-2 protein N]]''' - '''''AlphaFold2 Theoretical Model''''' - 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"/>.
-</StructureSection>
+'''[[SARS-CoV-2 protein ORF10]]''' - '''''AlphaFold2 Theoretical Model''''' - It is currently unclear whether this region translates into a functional protein<ref name="MIT_ColabFold"/><ref name="Zhang_Lab"/><ref name="Zhang"/>.
+== See also ==
+[[Coronavirus_Disease 2019 (COVID-19)]]<br>
+[[SARS-CoV-2_virus_proteins]]<br>
+__NOTOC__
 == References ==
 <references/>