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Finding low-energy conformations of lattice protein models by quantum annealing
Lattice protein folding models are a cornerstone of computational biophysics. Although these models are a coarse grained representation, they provide useful insight into the energy landscape of natural proteins. Finding low-energy threedimensional structures is an intractable problem even in the sim...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3417777/ https://www.ncbi.nlm.nih.gov/pubmed/22891157 http://dx.doi.org/10.1038/srep00571 |
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author | Perdomo-Ortiz, Alejandro Dickson, Neil Drew-Brook, Marshall Rose, Geordie Aspuru-Guzik, Alán |
author_facet | Perdomo-Ortiz, Alejandro Dickson, Neil Drew-Brook, Marshall Rose, Geordie Aspuru-Guzik, Alán |
author_sort | Perdomo-Ortiz, Alejandro |
collection | PubMed |
description | Lattice protein folding models are a cornerstone of computational biophysics. Although these models are a coarse grained representation, they provide useful insight into the energy landscape of natural proteins. Finding low-energy threedimensional structures is an intractable problem even in the simplest model, the Hydrophobic-Polar (HP) model. Description of protein-like properties are more accurately described by generalized models, such as the one proposed by Miyazawa and Jernigan (MJ), which explicitly take into account the unique interactions among all 20 amino acids. There is theoretical and experimental evidence of the advantage of solving classical optimization problems using quantum annealing over its classical analogue (simulated annealing). In this report, we present a benchmark implementation of quantum annealing for lattice protein folding problems (six different experiments up to 81 superconducting quantum bits). This first implementation of a biophysical problem paves the way towards studying optimization problems in biophysics and statistical mechanics using quantum devices. |
format | Online Article Text |
id | pubmed-3417777 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-34177772012-08-13 Finding low-energy conformations of lattice protein models by quantum annealing Perdomo-Ortiz, Alejandro Dickson, Neil Drew-Brook, Marshall Rose, Geordie Aspuru-Guzik, Alán Sci Rep Article Lattice protein folding models are a cornerstone of computational biophysics. Although these models are a coarse grained representation, they provide useful insight into the energy landscape of natural proteins. Finding low-energy threedimensional structures is an intractable problem even in the simplest model, the Hydrophobic-Polar (HP) model. Description of protein-like properties are more accurately described by generalized models, such as the one proposed by Miyazawa and Jernigan (MJ), which explicitly take into account the unique interactions among all 20 amino acids. There is theoretical and experimental evidence of the advantage of solving classical optimization problems using quantum annealing over its classical analogue (simulated annealing). In this report, we present a benchmark implementation of quantum annealing for lattice protein folding problems (six different experiments up to 81 superconducting quantum bits). This first implementation of a biophysical problem paves the way towards studying optimization problems in biophysics and statistical mechanics using quantum devices. Nature Publishing Group 2012-08-13 /pmc/articles/PMC3417777/ /pubmed/22891157 http://dx.doi.org/10.1038/srep00571 Text en Copyright © 2012, Macmillan Publishers Limited. All rights reserved http://creativecommons.org/licenses/by-nc-nd/3.0/ This work is licensed under a Creative Commons Attribution-NonCommercial-No Derivative Works 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/3.0/ |
spellingShingle | Article Perdomo-Ortiz, Alejandro Dickson, Neil Drew-Brook, Marshall Rose, Geordie Aspuru-Guzik, Alán Finding low-energy conformations of lattice protein models by quantum annealing |
title | Finding low-energy conformations of lattice protein models by quantum annealing |
title_full | Finding low-energy conformations of lattice protein models by quantum annealing |
title_fullStr | Finding low-energy conformations of lattice protein models by quantum annealing |
title_full_unstemmed | Finding low-energy conformations of lattice protein models by quantum annealing |
title_short | Finding low-energy conformations of lattice protein models by quantum annealing |
title_sort | finding low-energy conformations of lattice protein models by quantum annealing |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3417777/ https://www.ncbi.nlm.nih.gov/pubmed/22891157 http://dx.doi.org/10.1038/srep00571 |
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