[chimerax-users] getting AlphaFold predictions

[Elaine Meng]

Hi Yk,
Forwarding to chimerax-users at cgl.ucsf.edu since I don't have a good answer for this currently.

(We prefer you use that address for questions unless they include some data that needs to stay private.)
Thanks!
Elaine

> On Sep 9, 2021, at 1:57 PM, Yunsik Kang <kangy at ohsu.edu> wrote:
> 
> 
> Hi Elaine,
> 
> Thank you again!
> 
> I did open it and using ChimeraX I can see the pdb files and see the structure! It is amazing!
> 
> One question. 
> 
> Since my protein is massive and this is just parts of my protein, is there a way ChimeraX can stitch it all together?
> 
> Like Tristan says it is 1400 residues each, can I perhaps somehow stitch the whole thing together?
> 
> Yk
> 
> -----Original Message-----
> From: Elaine Meng <meng at cgl.ucsf.edu> 
> Sent: Thursday, September 9, 2021 8:12 AM
> To: Yunsik Kang <kangy at ohsu.edu>
> Cc: meng Elaine <meng at cgl.ucsf.edu>
> Subject: [EXTERNAL] Re: [chimerax-users] getting AlphaFold predictions
> 
> Hi Yunsik,
> I do not know the answer to your questions.  We are not the developers of AlphaFold or the AlphaFold database.  We only added tools in ChimeraX to connect to them.
> 
> Maybe there is information at the AlphaFold database about what's in their download.  I have never downloaded these myself.
> <https://www.alphafold.ebi.ac.uk/download>
> 
> All I know is that "tar" is a way of putting multiple files together and that you have to "untar" to get them apart.  This is a standard computer file thing, not related to any specific kind of files.
> 
> Usually if you doubleclick the tar file your computer will automatically untar it and make some new folder or folders containing the files. You would need to have enough space available on your computer for the large number of files.
> 
> I don't know how they are named but maybe there is a README file that comes with it, or if not, you may need to look at the files with a text editor.  Maybe they have the Uniprot IDs of the proteins somewhere in the names or header text of the file.
> 
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> On Sep 8, 2021, at 7:36 PM, Yunsik Kang <kangy at ohsu.edu> wrote:
>> 
>> Hi Elaine,
>> 
>> Thank you for the fast response. My proteins are not found in the Alphafold search.
>> 
>> I am new to this so bear with me. I downloaded the human TAR file as Tristan has said, but have no idea how to search or even start looking for my protein.
>> 
>> Could you help? Or is this something I need professional help with?
>> 
>> Would it help to tell you the protein I am interested in?
>> 
>> Thank you again.
>> Yunsik
>> 
>> From: Elaine Meng <meng at cgl.ucsf.edu>
>> Sent: Wednesday, September 8, 2021 3:44 PM
>> To: Yunsik Kang <kangy at ohsu.edu>
>> Subject: [EXTERNAL] Fwd: [chimerax-users] getting AlphaFold 
>> predictions
>> 
>> Forwarding in case you did not get Tristan's reply below:
>> 
>> 
>> Begin forwarded message:
>> 
>> From: Tristan Croll via ChimeraX-users <chimerax-users at cgl.ucsf.edu>
>> Subject: Re: [chimerax-users] getting AlphaFold predictions
>> Date: September 8, 2021 at 3:17:28 PM PDT
>> To: ChimeraX Users Help <ChimeraX-users at cgl.ucsf.edu>
>> Reply-To: Tristan Croll <tic20 at cam.ac.uk>
>> 
>> 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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> 
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