A compound having a polysaccharide binding domain such as contained by a cellulose and essentially lacking in polysaccharidase activity is purified from other ingredients in a mixture using an affinity partition system. A mixture containing the compound is contacted with a system containing as a first phase an aqueous solution of oligosaccharide polymer such as cellulose and as a second phase a solution of a polymer such as a poly(ethylene glycol)-poly(propylene glycol) copolymer. The compound petitions into the first phase and binds to the oligosaccharide polymer, preferably with a Ka of 103 to 107, to form a complex. The complex is collected, and the compound is dissociated from the oligosaccharide polymer. The compound may be formed of a non-peptide chemical moiety or a peptide moiety linked to a polypeptide having the polysaccharide binding domain. The compound may also be a fusion polypeptide containing the polysaccharide binding domain linked through a protease recognition sequence to a macromolecule such as an enzyme, a hormone or an antibody. The macromolecule can be removed by using a protease to cleave the recognition sequence. Another partition system contains the oligosaccharide polymer and a phase separation inducing agent such as a sulfate or citrate salt that induces separation to produce different phases.