The fixed-point algebraic method [Storer and Cornish-Bowden (1976) Biochem. J. 159, 1–5] for computing the concentrations at equilibrium of complex biochemical mixtures fails for many binding stoichiometries, especially those that include molecular self-association. A typical example is the monomer–dimer–tetramer equilibrium. This paper reports two main results. First, the above algorithm is analysed theoretically to predict for which binding stoichiometries it succeeds and for which it will fail. Secondly, an alternative algorithm is described for self-associating biochemical systems. Illustrative examples are based on the dimeric proteinase from HIV.

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