COVID-19 AlphaFold2 Models: Difference between revisions
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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"> | 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">[https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb MIT ColabFold]</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> | 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 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"> | '''[[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="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="Zhang_Lab"/><ref name="Zhang"/>. | ||