Skip to main content
. Author manuscript; available in PMC: 2021 Dec 8.
Published in final edited form as: J Chem Theory Comput. 2020 Nov 17;16(12):7895–7914. doi: 10.1021/acs.jctc.0c00830

Figure 13.

Figure 13.

Representative snapshots chosen from MSLD simulation trajectories. Panel a shows the ligand with cyclohexanol group (Site2-sub4) from the P38MK-7 system forming a water-mediated hydrogen bond with the protein. The snapshot coincides with the lambda value of the substituent depicted being close to unity. Panel b shows the tri-fluoro phenyl group (Site1-sub8) from HSP90–2 system. Top sub-panel shows a snapshot corresponding to the lambda value of Site1-sub8 being close to zero, and the bottom sub-panel corresponds to the group interacting with the protein with a lambda value close to unity. The circled region shows a change in the protein conformation to accommodate the tri-fluoro group.