The major conformation for apo PTP1B is the inactive conformation, in agreement with experimental results that suggest a low fraction of active states (2.5%) ("apo" in Figure ) . Upon substrate binding there is a significant increase in active conformation probability, in agreement with experimental data ("reference" in Figure ). However while NMR measurements suggest the active conformation dominates PTP1B's conformational ensemble when the enzyme is bound to a substrate (87% population ), the MSM indicates the active state is only formed 25% of the time. Experimental data suggests that activation of PTP1B by closure of the WPD loop is coupled with a disorder-to-order transition of helix α7. Owing to the difficulties in reliably simulating such large-scale conformational changes the PTP1B model used in the current study is a truncated variant that lacks helix α7. Experimental evidence shows that a mutant PTP1B-∆7 lacking helix α7 is about 40% less active than wild-type . Thus the incomplete activation of PTP1B in presence of a model peptide substrate is fully consistent with experimental observations. The goal of the present protocol is to classify ligands as allosteric effectors by comparison of relative shifts in active state populations, for which trends (relative to the reference system) are sufficient.