In order to computationally characterize the (pro)cathepsin/glycosaminoglycan complexes, one has to i) retrieve structures of ligand and receptor; ii) predict the structures of a complexes; iii) examine how the complexes behave in time; iv) estimate the complexes stabilities. Computational analysis of procathepsin complexes with glycosaminoglycans requires application of several approaches. First, procathepsin structures which are accessible from Protein Data Bank will be subjected to molecular dynamics simulations with the coarse-grained UNRES force field in order to get a deeper view on conformational ensemble of those proteases. Glycosaminoglycan structures, on the other hand, can be modeled. Using those models, complex structures can be calculated with use of the molecular docking method. Performing cluster analysis and picking most representative structures from each of the clusters, the calculated complex structures can be simulated by the molecular dynamics approach in order to study evolution of a system over time. Post-processing free energy analysis of the produced molecular dynamics trajectories by various approaches such as Molecular Mechanics-Poisson Boltzmann with the entropy calculations by normal mode, quasi harmonic analysis or potential of mean force approach can provide us valuable data on the stability of the complex. Moreover, additional per-residue analysis of free energy can identify aminoacid residues that contribute mostly to the interactions between receptor and ligand and in turn – to overall stability of a complex.