Protocols

To predict GPCR-ligand complex structures, use AlphaFold-template biasing for receptor and flexible docking tool like GALD. For peptide docking, use AlphaFold-multimer with recycle number 10.

AlphaFold-Multimer has limitations in antibody-antigen complex structure prediction, although AlphaFold2 predicts each monomer structure accurately. GalaxyTongDock, an ab initio docking tool, could be a solution for some problems when used with proper options.

For large biomolecular complexes, experimental structures for composing units and in silico complex modeling could be combined to unveil their behavior. Deep-learning based modeling such as AlphaFold-multimer and an ab initio docking tool such as GalaxyTongDock could help researchers to predict structures corresponding to different states.