Modeling glycans with AlphaFold 3: capabilities, caveats, and limitations.

ABSTRACT: Glycans are complex carbohydrates that exhibit extraordinary structural complexity and stereochemical diversity while playing essential roles in many biological processes, including immune regulation, pathogen recognition, and cell communication. In humans, more than half of all proteins are glycosylated, particularly those in secretory and membrane-associated pathways, highlighting the importance of glycans in health and disease. The recent release of the AlphaFold 3 source code enables customizable modeling not only of proteins but also glycan-containing biomolecular complexes. We assessed the capacity of AlphaFold 3 to model glycans using several input formats and identified a hybrid syntax employing Chemical Component Dictionary (CCD)-based molecular building blocks linked by "bondedAt

SUBMITTER: Huang C 

PROVIDER: S-EPMC12448869 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature