COVID-19 AlphaFold2 Models: Difference between revisions

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Joel L. Sussman (talk | contribs)
ConfirmAccount, Editor, Mutation, Print3D, Tester, Bureaucrats, journal, tester
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Joel L. Sussman (talk | contribs)
ConfirmAccount, Editor, Mutation, Print3D, Tester, Bureaucrats, journal, tester
11,713 edits
No edit summary
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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|900px|left|thumb|SARS-CoV-2 Protein Organization, from Gordon
{{Theoretical_model}}
et al. & Krogan (2020)<ref>DOI: 10.1101/2020.03.22.002386</ref> )]]
{{Template:ModelConfidence}}
[[Image:VirusImage.jpg|right|280px|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">[https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb  MIT ColabFold]</ref>, which was developed by [https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb 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. [[AlphaFold]]2 was used to predict these structures using the MIT ColabFold server<ref name="MIT_ColabFold"/>. 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>
<br>
{{Template:COVID Validation}}
 
 
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">[https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb  MIT ColabFold]</ref>, which was developed by [https://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>




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