Molecular unfolding formulation with enhanced quantum annealing approach
- URL: http://arxiv.org/abs/2403.00507v1
- Date: Fri, 1 Mar 2024 13:09:46 GMT
- Title: Molecular unfolding formulation with enhanced quantum annealing approach
- Authors: Arit Kumar Bishwas, Arish Pitchai, Anuraj Som
- Abstract summary: Molecular unfolding problem aims to find the torsional configuration that increases the inter-atomic distance within a molecule.
Quantum annealing approach first encodes the problem into a Higher-order Unconstrained Binary Optimization (HUBO) equation.
The resultant HUBO is then converted to a Quadratic Unconstrained Binary Optimization equation (QUBO)
- Score: 0.0
- License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
- Abstract: Molecular docking is a crucial phase in drug discovery, involving the precise
determination of the optimal spatial arrangement between two molecules when
they bind. The such analysis, the 3D structure of molecules is a fundamental
consideration, involving the manipulation of molecular representations based on
their degrees of freedom, including rigid roto-translation and fragment
rotations along rotatable bonds, to determine the preferred spatial arrangement
when molecules bind to each other. In this paper, quantum annealing based
solution to solve Molecular unfolding (MU) problem, a specific phase within
molecular docking, is explored and compared with a state-of-the-art classical
algorithm named "GeoDock". Molecular unfolding focuses on expanding a molecule
to an unfolded state to simplify manipulation within the target cavity and
optimize its configuration, typically by maximizing molecular area or internal
atom distances. Molecular unfolding problem aims to find the torsional
configuration that increases the inter-atomic distance within a molecule, which
also increases the molecular area. Quantum annealing approach first encodes the
problem into a Higher-order Unconstrained Binary Optimization (HUBO) equation
which is pruned to an arbitrary percentage to improve the time efficiency and
to be able to solve the equation using any quantum annealer. The resultant HUBO
is then converted to a Quadratic Unconstrained Binary Optimization equation
(QUBO), which is easily embedded on a D-wave annealing Quantum processor.
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