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. Author manuscript; available in PMC: 2018 Apr 20.
Published in final edited form as: J Phys Chem B. 2017 Mar 3;121(15):3597–3606. doi: 10.1021/acs.jpcb.6b09388

Figure 2.

Figure 2

Panel A: before beginning the simulations, benzamidine has been placed along each of the milestones in gradually increasing distances from the center of the binding site on trypsin. Panel B: The center-of-mass of the benzamidine molecule in the trypsin 3PTB crystal structure lies within the lowest 1Å milestone (red sphere), which we define as the bound state