Calculation of substrate binding affinities for a bacterial GH78 rhamnosidase through molecular dynamics simulations

- Structural model of rhamnosidase Ram2 of Pediococcus acidilactici.
- Calculated binding free energies of rutinose and p-NPR agree with experiments.
- Suggested binding poses of rutinose and p-NPR are distinctly different.
- Different binding poses of rutinose and p-NPR are supported by experiments.
- Active site residues are proposed for further mutagenesis studies