Hi Elaine and Tom,

Thanks for the clarification. As you mentioned, an older Alphafold2 was used to predict the structures of the AF database; this might be the reason for the structural differences between the two structures from the same sequence. Also, I did the superimposition of the AF database predicted structure of that protein with the predicted structures of related proteins using the built-in AlphaFold of ChimeraX; they don't overlap that much. However, in the superimposition of the predicted protein structure using built-in AlphaFold of ChimeraX with those related proteins, I found several overlapping regions and similar orientations with those proteins.

Best,

Raihan

On Fri, 12 Jul 2024 at 16:19, Tom Goddard <goddard@sonic.net> wrote:

Hi Raihan,

As Elaine points out there are many reasons that the AlphaFold database structure may differ from an AlphaFold prediction made on Google Colab using ChimeraX. One general observation is that when you get different AlphaFold predictions for the same sequence it is usually the case that AlphaFold has low confidence.

Here are a few more observations. The AlphaFold database structure were predicted with an older AlphaFold 2 a few years ago and only one model instead of 5 were predicted since they needed to save time since they were predicting 200 million structures. With Google Colab it predicts 5 models using 5 different networks and ChimeraX shows you the best confidence one although all 5 are downloaded and you can look at them.

Google Colab sets up a virtual machine to run the prediction each time so it does not download the 2 Tbytes of sequence data used by the full AlphaFold, and instead only used about 100 Mbytes of sequence data, and it uses no structure templates.

Because of all the many differences in how AlphaFold is run it certainly won't produce exactly the same result, but usually if it has high confidence the different methods predict almost the same structure conformation.

None of these methods use AlphaFold 3 because Google has not released the code so you can only run that using Google's AlphaFold 3 server.

Tom