[chimerax-users] getting AlphaFold predictions

[Tristan Croll]

The human protein will be in the EBI-Alphafold2 database, but not accessible to the search tool. For human proteins (and only human, so far) longer than ~2000 residues, the predictions are provided as multiple 1400-residue fragments starting at residue 1, 201, etc.. The only way to get those right now is to download the tarball of the complete set of human protein predictions, and find them in there.

> On 8 Sep 2021, at 23:08, Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Yunsik,
> I don't know where/how you can run a prediction for such a long sequence, maybe others can comment on that.  However:
> 
> First make sure there is not already a predicted structure for that protein in the AlphaFold Database!  E.g. try the Search button on the AlphaFold tool and see if the same UniProt entries as you are interested in are found.   The database includes human and other well-studied species (maybe also the yeast you mentioned, depending on the exact species).   If the prediction is already in the database, there is no need to run a new calculation.
> 
> ChimeraX AlphaFold tool:
> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Sep 8, 2021, at 2:45 PM, Yunsik Kang via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>> 
>> Hello,
>> 
>> My name is Yunsik Kang, and I am a postdoc in Marc Freeman’s lab at the Vollum Institute.
>> 
>> I would love to use ChimeraX to predict the structure of my protein of interest. I watched all the YouTube videos and tried to run the program.
>> 
>> Unfortunately, my protein is 5005 amino acids in humans and 2958 aa in yeast. I get a message “Please use the full AlphaFold system for long sequences.”
>> 
>> My question is what is the best way to approach this problem? Should I cut the protein in half and run the program? In one of the videos, it mentions after 700 aa it will have problems. Will it work if I get Colab-Pro? Or would the server crash no matter what.
>> 
>> I am not a structural biologist, but I hope the structure can help be predict me with my research.  
>> 
>> Thank you,
>> Yunsik
> 
> 
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