Hierarchical representation of molecular species in Meredys. (A) Two independent clusters each composed of one entity, E1 and E2, prior to bond formation. Large blue spheres represent the stokes radii of the clusters. Green disks represent the points of binding (B) A new cluster composed of two entities, E1 and E2 resulting from the assembly of the former clusters by reaction of reaction points S1 and R1. The stokes radius of the new cluster is composed of the stokes radii of all the composing entities. Yellow points P1 & P2, particles centre of mass; purple points E1 & E2, entities centre of mass; blue point C1, cluster centre of mass; red points S1, S2, S3 & R1, reaction points.
Tolle and Le Novère BMC Systems Biology 2010 4:24 doi:10.1186/1752-0509-4-24