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

20 June 2019, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


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.


molecular docking
molecular dynamics
computer-assisted drug design
peptide docking


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