Protein–Glycan Docking

At Profacgen, we predict these protein–carbohydrate interactions through the combination of a genetic conformational search algorithm coupled with an empirical free energy function specific for carbohydrates. Our docking procedure allows for a systematic exploration of the orientations and positions of carbohydrate ligand into a protein cavity (which is usually more open and less well defined compared to small molecule binding sites), and assesses free energies of complex formation. Experiment-derived constraints can also be applied to the docking protocol to restrict the search space for the sugar as well as the protein molecule. The energy function is specifically designed for carbohydrates, which is used for the clustering of binding poses and exploration of the most energetically favorable complex structure. The relative stability of protein ligand complexes can be further evaluated by performing a short molecular dynamics simulation run.

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