Table 2

State Space Transformation for scaffold with three binding domains. Transformation for a scaffold protein with 3 binding domains. The transformation is hierarchically structured and introduces macroscopic quantities like the overall concentration of R and the levels of occupancy of each domain (z0 to z3), mesoscopic quantities describing pairs of concurrently occupied domains (z4 to z6) and microscopic quantities corresponding to individual multiprotein species (z7).

z0 = R[0, 0, 0] + R[1, 0, 0] + R[0, 1, 0] + R[0, 0, 1] + R[1, 1, 0] + R[1, 0, 1] + R[0, 1, 1] + R[1, 1, 1]     (52a)

z1 = R[1, 0, 0] + R[1, 1, 0] + R[1, 0, 1] + R[1, 1, 1]     (52b)

z2 = R[0, 1, 0] + R[1, 1, 0] + R[0, 1, 1] + R[1, 1, 1]     (52c)

z3 = R[0, 0, 1] + R[1, 0, 1] + R[0, 1, 1] + R[1, 1, 1]     (52d)

z4 = R[1, 1, 0] + R[1, 1, 1]     (52e)

z5 = R[1, 0, 1] + R[1, 1, 1]     (52f)

z6 = R[0, 1, 1] + R[1, 1, 1]     (52g)

z7 = R[1, 1, 1]     (52h)


Conzelmann et al. BMC Bioinformatics 2006 7:34   doi:10.1186/1471-2105-7-34

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