Excited to share our new AllMetal3D model building on Metal3D. AllMetal3D predicts the location, identity and geometry of the major biologically relevant metal ions https://doi.org/10.1101/2025.02.05.636627
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We compared to a few other tools that perform either metal identity prediction or location prediction and found that is very important to include negative classes during training and also cluster metal ions by biological similarity.
In earlier work, we already analyzed how AllMetal3D given a structural input and no information about metal stoichiometry fares against co-folding methods given metal stoichiometry but no structure: https://doi.org/10.1101/2024.05.28.596236
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ChimeraX: https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxallmetal3d
HuggingFace: https://huggingface.co/spaces/simonduerr/allmetal3d
Docs for Python Package:
https://lcbc-epfl.github.io/allmetal3d/