I suspect many people have been anticipating this, whilst AlphaFold was a great step forward in predicting protein 3D structure it did have significant limitations.
RoseTTAFold All-Atom is capable of predicting the structures of all atoms of a biological unit, including:
▪ proteins
▪ nucleic acids
▪ small molecules
▪ metals
▪ covalent modifications (covalently modified proteins)
RFdiffusionAA, builds protein structures around small molecules. Starting from random distributions of amino acid residues surrounding target small molecules. The model returns two files:
PDB file with predicted structure (bfactors represent predicted lddt at each position)
pytorch file with confidence metrics stored
https://doi.org/10.1126/science.adl2528
The code is on GitHub although at present there are no license details.
https://github.com/baker-laboratory/RoseTTAFold-All-Atom