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 exploratory, see below for specifc examples. Also take a look at complementary work: KosinskiLab/af3x and bio-phys/polyUb-AF.

1AAR 1AAR with (left, RMSD<1) vs without (right, RMSD>10) covalent bond between Lys48 and Gly76, AlphaFold3 run without templates

Quick start

pip install alphafold3-polymer-bonds
alphafold3_polymer_bonds --help

Metadata

Release files for alphafold3-polymer-bonds 0.3

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Source distribution for alphafold3-polymer-bonds 0.3
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Uploaded via	`twine/6.1.0 CPython/3.11.6`

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