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Selective_Ligand_Induced_Conformational_Ensemble__SLICE__Dynamics.pdf (1.6 MB)

Accelerated Molecular Dynamics for Structural Prediction in Protein/Peptide Binding: The SLICE Method

submitted on 19.06.2019 and posted on 20.06.2019 by James McFarlane, Katherine Krause, Irina Paci
The work in this submission presents a molecular simulation technique that is able to overcome induced-fit binding issues with a uniquely challenging binding site. This method differs from commercially available methods in that we use a combined software approach that allows users to patch together inexpensive and academically available programs. Our method also differs fundamentally in how the potential energy of the interaction is explored and lends itself to the success in modeling our test system. As an added benefit, our test system is CBX8, an epigenetic reader protein and speculative target for chemotherapy. The method was not only successful in matching crystal structure data, but uncovered a number of induced-fit structural features of the binding motif that are useful in the design of potential inhibitors for this protein.


Email Address of Submitting Author


University of Victoria



ORCID For Submitting Author


Declaration of Conflict of Interest