Quantum molecular unfolding

  title={Quantum molecular unfolding},
  author={Kevin Mato and Riccardo Mengoni and Daniele Ottaviani and Gianluca Palermo},
  journal={Quantum Science \& Technology},
Molecular docking is an important step of the drug discovery process which aims at calculating the preferred position and shape of one molecule to a second when they are bound to each other. During such analysis, 3D representations of molecules are manipulated according to their degree of freedoms: rigid roto-translation and fragment rotations along the rotatable bonds. In our work, we focussed on one specific phase of the molecular docking procedure i.e. molecular unfolding (MU), which is used… 

QuAnt: Quantum Annealing with Learnt Couplings

This paper proposes to learn QUBO forms from data through gradient backpropagation instead of deriving them, and demonstrates the advantages of learnt QUBOs on the diverse problem types of graph matching, 2D point cloud alignment and 3D rotation estimation.

Optimizing the Production of Test Vehicles using Hybrid Constrained Quantum Annealing

This paper models the problem in the framework of satisfiability and solves it by utilizing the newly introduced hybrid constrained quadratic model (CQM) solver provided by D-Wave and concludes that the performance of the CQM solver is comparable to classical solvers in optimizing the number of test vehicles.

Multibody molecular docking on a quantum annealer

Molecular docking, which aims to find the most stable interacting configuration of a set of molecules, is of critical importance to drug discovery. Although a considerable number of classical

A Review on Parallel Virtual Screening Softwares for High-Performance Computers

As the problem is to find the most stable (global) minima for numerous protein–ligand complexes (on the order of 106 to 1012), the parallel implementation of in silico virtual screening can be exploited to ensure drug discovery in affordable time.



Tunable approximations to control time-to-solution in an HPC molecular docking Mini-App

This work improves the geometric approach to molecular docking by introducing tunable approximations and modelled time-to-solution of the virtual screening task as a function of software knobs, input data features, and available computational resources.

A Variable Neighbourhood Descent Heuristic for Conformational Search Using a Quantum Annealer

A variable neighbourhood search heuristic using the structure of a molecule to allow for the efficient use of a binary quadratic optimizer for conformational search, which is flexible with respect to the choice of molecular force field and the number of discretization levels in the search space.

Coarse-grained lattice protein folding on a quantum annealer

This work sets a new record for lattice protein folding on a quantum annealer by folding Chignolin on a planar lattice and Trp-Cage on a cubic lattice.

Molecular docking: a powerful approach for structure-based drug discovery.

This review presents a brief introduction of the available molecular docking methods, and their development and applications in drug discovery, and a recently developed local move Monte Carlo based approach is introduced.

Comparative evaluation of eight docking tools for docking and virtual screening accuracy

The current study pinpoints some physicochemical descriptors of either the ligand or its cognate protein‐binding site that generally lead to docking/scoring inaccuracies.

The PDBbind database: methodologies and updates.

The PDBbind database is developed to provide a comprehensive collection of binding affinities for the protein-ligand complexes in the Protein Data Bank, and a total of 900 complexes were selected to form a "refined set", which is of particular value as a standard data set for docking and scoring studies.

Adiabatic Quantum Computation and Quantum Annealing: Theory and Practice

  • Catherine C. McGeoch
  • Physics
    Adiabatic Quantum Computation and Quantum Annealing: Theory and Practice
  • 2014
This monograph presents an introductory overview of Adiabatic quantum computation, a survey of basic principles of quantum computation and what is known about the AQC model and the QA algorithm paradigm, and reviews the D-Wave technology stack.

Structure-based virtual screening: an overview.

  • P. Lyne
  • Biology
    Drug discovery today
  • 2002

Domain wall encoding of discrete variables for quantum annealing and QAOA

In this paper I propose a new method of encoding discrete variables into Ising model qubits for quantum optimisation. The new method is based on the physics of domain walls in one-dimensional Ising

Power of Pausing: Advancing Understanding of Thermalization in Experimental Quantum Annealers

We investigate alternative annealing schedules on the current generation of quantum annealing hardware (the D-Wave 2000Q), which includes the use of forward and reverse annealing with an intermediate