Furanosides have been subjected to extensive studies owing to their inherent flexibility, which is believed to play an important role in the survival and pathogenicity of different disease-causing organisms in the human body. This study reports the binding free energy (Delta G) and specificity of arabinofuranose oligosaccharides to a protein, arabinanase (Arb43A), with the use of potential of mean force (PMF) calculations using the umbrella-sampling simulations. Long molecular dynamics simulations have been carried out to understand intermolecular interactions in the arabinofuranose-protein complex. The PMF for pulling the alpha-(1 -> 5)-linked L-arabinohexaose (ligand) from the protein provides a large free energy of binding, -16.8 kcal/mol. The Delta G of the nonreducing arabinotriose end is found to be -12.6 kcal/mol, while the Delta G of the reducing end is calculated to be -7.7 kcal/mol. In the absence of nonreducing arabinotrioside, the Delta G of the reducing arabinotrioside is -8.5 kcal/mol. Similarly, in the absence of reducing arabinotrioside, the Delta G of the nonreducing arabinotrioside is calculated to be -9.4 kcal/mol. The main contributing factor in the protein-arabinofuranose binding is hydrogen bonding. Acidic amino acid residues, Glu and Asp, with furanosides produce the strongest hydrogen bonding. Araf-A, B, and C construct the reducing arabinotriose, while Araf-D, E, and F construct the nonreducing arabinotriose. Since most of the hydrogen-bonding occupancies belong to Araf-D and Araf-E, the nonreducing arabinotriose is bound to protein more strongly than the reducing arabinotriose. This explains why the reducing arabinotriose can detach from the protein in nature.