Qiskit Global Hackaton 2021

VARIATIONAL QUANTUM CIRCUITS IN A PROTEIN NETWORK GRAPH

To map biochemical interactions inside a 3D-protein structure into a graph network to find bounding amino acids function using a VQA

Objectives

• To find bounding amino acids function on a delimited network graph approach that characterized a chemical structure using a variational quantum circuit.
• To apply quantum circuits used in graph theory and optimization problems to map 3D-protein structure into chemical interaction network.
• Using the QAOA variational form to find an approximate solution for the protein folding quadratic program.
• To encourage people to push into quantum computing and solve real molecular biology problems faster than classical methods.

With number of atoms in the molecule (YA., A., and HA, 2006).

• Hydrophobic.Disulfide (bridnge)
• Hydrogen bonds
• Ionic and aromatic (partial)
• Cation-π.Peptide bond

Graph network methodology

Graph network of 1Plxa. Each edge corresponds to one of the following biochemical interactions:

• Hydrophobic
• Disulfide (bridnge)
• Hydrogen bonds
• Ionic and aromatic (partial)
• Cation
• Peptide bond

First we represent Amino Acids asnodes of graph network. Then we perform its graph reduction.

Classic solution

We implement a classical solution using the algorithm travelingsalesman as an NP-complete problem. for protein folding problembased on a protein network graph to find bounding amino acids, themain objective is to find the nodes with more interactions orweights (proteins with more connections)

Brute force Approach

Quantum Computing Approach

Protein folding problem base on the travelling salesman.