What is it about?
SiteAF3 is a universal molecular interaction modeling platform based on AlphaFold3, supporting structure prediction and analysis for various receptor-ligand type combinations. It can fix the structure of receptor and only fold ligands through modifying the diffusion module in AlphaFold3.
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Photo by National Cancer Institute on Unsplash
Why is it important?
SiteAF3 is a generalized, high-accuracy, site-specific modeling tool that significantly enhances AlphaFold3’s performance. SiteAF3 is extremely useful when modeling orphan protein (with known structures) and ligand interaction, as well as allosteric site and drug complexes.
Perspectives
I hope this article provides a useful tool for modeling complexes and a new aspect for large deep learning models in science like AlphaFold3. We can do a lot of interesting work based on large models. We discussed the limitation of MSA as well in the paper, which reveals the overfitting problem of AlphaFold3.
Haocheng Tang
University of Pittsburgh
Read the Original
This page is a summary of: Accurate site-specific folding via conditional diffusion based on AlphaFold3, Proceedings of the National Academy of Sciences, October 2025, Proceedings of the National Academy of Sciences,
DOI: 10.1073/pnas.2521048122.
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