Support for covalent bonds between/within polymer chains (protein, DNA, RNA) in AlphaFold3
Project description
Polymer bonds in AlphaFold3
AlphaFold3 does not allow covalent bonds between/within polymer chains (protein, DNA, RNA). We work around this limitation by treating one of the corresponding residue or nucleic acid as a modified residue/amino-acid. In principle, this may enable AlphaFold3 to explicitly model e.g. disulfide bonds, cyclic peptides, zero-length crosslinkers, protein-DNA bonds..
This is currently experimental/work-in-progress, please also have a look at complementary approaches KosinskiLab/af3x and bio-phys/polyUb-AF.
Quick start
git clone git@github.com:jurgjn/alphafold3-polymer-bonds.git
cd alphafold3-polymer-bonds
pip install -e .
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