Check what the reduction changes
The declared operation merges rapidly exchanging macrostates, then compares a remaining slow relaxation timescale with the original model. It takes transition and stationary models as inputs. A smaller state count is useful only when the dynamics relevant to the question survive.
Work alongside established kinetic modeling
Markov-state-model tools such as deeptime already estimate, analyze and coarse-grain dynamics. BioTwin’s proposed use connects its slow-mode check to ensemble representations and downstream landscape questions. A binding-state comparison could then retain both a reduced model and the evidence for accepting that reduction. A competent conventional MSM workflow is the appropriate comparison for any claim of saved work.
Conformations alone do not supply a clock
This reduction method is under development. Related kinetic calculations are implemented, while the reduction’s scientific performance still needs evaluation. Arbitrary or uniform transitions between structural conformers do not establish molecular rates. Start from a defensible trajectory or kinetic model, and compare retained timescales and transitions on held-out data.