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. Author manuscript; available in PMC: 2022 Jan 12.
Published in final edited form as: J Chem Theory Comput. 2020 Dec 8;17(1):302–314. doi: 10.1021/acs.jctc.0c00752

Figure 4:

Figure 4:

Restraints are included in the NCMC switching protocol. In order to keep the ligand in the binding site while the ligand’s interactions are off, an orientational restraint is used which corresponds to the dart that the ligand is in at the beginning of an NCMC move proposal. At the middle of the NCMC protocol, a MolDarting move is performed, and the restraint switches to a new orientational restraint corresponding to the new dart, which is subsequently turned off throughout the rest of the protocol.