Changes between Version 8 and Version 9 of SOPs/AlphaFold


Ignore:
Timestamp:
04/23/24 06:59:27 (9 months ago)
Author:
twhitfie
Comment:

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  • SOPs/AlphaFold

    v8 v9  
    66=== Running AlphaFold using ChimeraX ===
    77
    8 If you cannot find a predicted structure for your protein within the databases listed above, perhaps because amino acid substitutions relative to the reference sequence are present, [https://www.cgl.ucsf.edu/chimerax/ ChimeraX] is an [https://www.youtube.com/watch?v=gIbCAcMDM7E easy place to start due to its graphical user interface] and convenient visualization tools.  You will need to install ChimeraX on a desktop or laptop computer, but the AlphaFold predictions will be made using computing resources in the cloud.
     8If you cannot find a predicted structure for your protein within the databases listed above, perhaps because amino acid substitutions relative to the reference sequence are present, [https://www.cgl.ucsf.edu/chimerax/ ChimeraX] is an [https://www.youtube.com/watch?v=gIbCAcMDM7E easy place to start due to its graphical user interface] and convenient visualization tools.  You will need to install ChimeraX on a desktop or laptop computer, but the AlphaFold predictions will be made using computing resources in the cloud via the [https://www.nature.com/articles/s41592-022-01488-1 ColabFold] implementation of AlphaFold, which uses [https://www.nature.com/articles/nbt.3988 MMseqs2] to efficiently compute an initial multiple sequence alignment.
    99
    1010=== Running AlphaFold using computing resources at Whitehead ===