Changes between Version 1 and Version 2 of SOPs/AlphaFoldMultimer


Ignore:
Timestamp:
04/23/24 06:52:15 (9 months ago)
Author:
twhitfie
Comment:

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  • SOPs/AlphaFoldMultimer

    v1 v2  
    1 == Predicting protein structure from sequence using AlphaFold ==
     1== Using AlphaFold multimer to predict the structure of protein complexes ==
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    33=== Background ===
    4 The success of [https://www.nature.com/articles/s41586-021-03819-2 DeepMind's AlphaFold protein folding algorithm] in the CASP14 structural prediction assessment has been widely celebrated and has profoundly invigorated the structural biology community. Today, if you have a protein sequence for which you'd like to learn a high quality predicted structure, an excellent place to start is the [https://alphafold.ebi.ac.uk/ AlphaFold Protein Structure Database]. An alternative database to search is the [https://esmatlas.com/resources?action=fold ESM Metagenomic Atlas], where you may find predicted structures for orphan proteins with few sequence homologs.
     4As soon as the effectiveness of AlphaFold2 for protein structure prediction became evident, workers began to adapt it to predicting protein structure <em> complexes </em>.  This effort led to [https://www.biorxiv.org/content/10.1101/2021.10.04.463034v2 AlphaFold-Multimer]. While the best place to start a search for a predicted structure for a single protein sequence is likely to be an online database, you will likely have to compute the predicted structures for multimeric protein complexes.
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    6 === Running AlphaFold using ChimeraX ===
     6=== Running AlphaFold-Multimer using ChimeraX ===
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    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.
     8As with structure prediction for monomeric proteins, [https://www.cgl.ucsf.edu/chimerax/ ChimeraX] is a good [https://www.youtube.com/watch?v=6lXeCPuTePs starting point due to its intuitive 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.
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    1010=== Running AlphaFold using computing resources at Whitehead ===