[QUEST]

I have been working on the disaccharide-binding proteins, but I am currently stuck on the RF3 step. I have tried multiple times, but I get the same outcome every time: RoseTTAFold3 cannot recognize a disaccharide molecule as a single entity.
The core problem is that, in the PDB format, most disaccharides are treated as two separate monosaccharides. However, when I tried to provide the SMILES or CCD code or SDF file of the disaccharide to RF3, it generated protein structures with two monosaccharides spaced apart, and, of course, this configuration negatively affects the protein folding. During the model generation, RF3 also compares the models with the backbones generated by RFD3 (where there is the disaccharide)

Start by tracing the RF3 input path for PDB, SMILES, CCD, and SDF inputs, then compare it with the RFD3 backbone-generation path. Reproduce the disaccharide case described here and inspect where the two monosaccharides become separate entities. Done means a supported input keeps the disaccharide connected during RF3 model generation and comparison.