A computer program for the analysis of protein complex formation

MOTIVATION We needed an efficient way to explore the binding reactions leading to protein complexes of known composition and structure. RESULTS A new program is described that allows the user to define a set of protein elements and to link these elements into an oligomeric 'ball-and-stick' assembly in a graphical interface. Once the structure of the oligomer has been defined, the program then employs a novel algorithm to deduce the binding reactions and intermediate complexes needed to make the oligomer from its starting protein components. The program also finds the equilibrium state of the system, using either default starting concentrations and Kd values or data supplied by the user.