A phosphorilated peptide (initially red) has been recognized and "captured" at the surface of a "Src Homology 2 domain", or SH2 (grey). This event lies at the beginning of a complex series of reactions which affect the cell. In practice, the cell "responds" to external changes by "feeling" them when a SH2 becomes associated to a phosphorilated ligand. Studying the strength and dynamics of this binding is therefore extremely important. The picture shows snapshots in the course of one such "virtual experiment": a procedure, called steered molecular dynamics (SMD), which forces the tyrosine to be detached from the SH2 in a precisely controlled sequence (in color scale).

Simulation performed with the support of the volunteers of gpugrid.net.
Rendered with vmd and gelato. More details here.