Correlation between AF3 predicted scores and AF3Score

[LinearParadox]

Hi all,

I was curious about this tool and it would be tremendously helpful in our research. We were wondering if there is a benchmark against the scores output by alphafold3?

For example, given complexes 1,2,3,4,5 are the ipTMs generated with this tool comparable to those generated with AF3?

Additionally, if we already have AF3 jsons that have the MSA information in them, is there a way to easily input it into this tool?

Thanks!

[robertttlau]

Hi! Thank you for your interest in this tool.

Regarding the AF3 benchmark: We haven't tested the correlation between our tool's scores and AlphaFold3's output yet. We'd encourage you to test this on your systems of interest and welcome you to share your results with the community.

Regarding using existing AF3 JSONs with MSA: Yes, AF3 JSON files with MSA information can be directly input into this tool without any modification.

Hope this helps!