Hi Sara,

It is not very practical and not likely to be useful to predict a 5400 amino acid protein. It probably could be done if you had access to an Nvidia A100 GPU with 80 Gbytes of memory and were willing to wait about 50 hours for the prediction of the standard 5 structures. But the results would almost certainly be a jumble of domains packed incorrectly. Here are some runtimes of predictions using AlphaFold

https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html

The time goes up rapidly with number of amino acids, 1200 can be done in 2 hours, but 2400 takes about 12 hours.

Using ChimeraX it is probably possible to predict about 4000 amino acids if you use a paid Google Colab account with an A100 GPU and the maximum session time they allow of 24 hours at a cost of about $40 for one run. Here's a video on how you use a paid Google Colab account to run big AlphaFold predictions in ChimeraX

https://youtu.be/H-pDs9rZtkw

The main thing you should consider though is that the result will almost certainly not be useful. While AlphaFold makes nice predictions of small proteins (< 1000 amino acids) of one or a few domains, it rarely can make sense of proteins with lots of domains.

You didn't say what protein you are interested in so it is hard to advise since I don't know its domain structure. But if you are interested in how the truncated domains fold you might run just the terminal half-truncated domain and compare the prediction to the full domain. Or if there are a few domains that get truncated you might predict just those domains, or those in combination with the ones it is know to interact with if the total number residues and domains is feasible.

Tom

On Sep 3, 2023, at 2:15 PM, Sara Qubisi via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Hello Chimerax team.

I am a postdoc at SICKKIDS hospital, and I am currently working on a project that involves large protein (~5400 aa). I am new to Alphafold and Chimerax and I want to perform a structure comparison between the wild type protein and a set of frameshift mutation (result in protein truncation) versions of the protein. I learned online and from your YouTube videos that I cannot enter more than 1200aa per assay request. Is there a way to overcome this where I can use the full protein sequence.

Regards, Sara Qubisi.

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