NMR assignment through linear programming

José F.S. Bravo-Ferreira; David Cowburn; Yuehaw Khoo; Amit Singer

doi:10.1007/s10898-021-01004-3

NMR assignment through linear programming

José F.S. Bravo-Ferreira, David Cowburn, Yuehaw Khoo, Amit Singer

Biochemistry

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Abstract

Nuclear Magnetic Resonance (NMR) Spectroscopy is the second most used technique (after X-ray crystallography) for structural determination of proteins. A computational challenge in this technique involves solving a discrete optimization problem that assigns the resonance frequency to each atom in the protein. This paper introduces LIAN (LInear programming Assignment for NMR), a novel linear programming formulation of the problem which yields state-of-the-art results in simulated and experimental datasets.

Original language	English (US)
Pages (from-to)	3-28
Number of pages	26
Journal	Journal of Global Optimization
Volume	83
Issue number	1
DOIs	https://doi.org/10.1007/s10898-021-01004-3
State	Published - May 2022

Keywords

Linear programming relaxation
NMR spectroscopy
Resonance assignment problem
Shortest path problem

ASJC Scopus subject areas

Computer Science Applications
Control and Optimization
Management Science and Operations Research
Applied Mathematics

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10.1007/s10898-021-01004-3

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title = "NMR assignment through linear programming",

abstract = "Nuclear Magnetic Resonance (NMR) Spectroscopy is the second most used technique (after X-ray crystallography) for structural determination of proteins. A computational challenge in this technique involves solving a discrete optimization problem that assigns the resonance frequency to each atom in the protein. This paper introduces LIAN (LInear programming Assignment for NMR), a novel linear programming formulation of the problem which yields state-of-the-art results in simulated and experimental datasets.",

keywords = "Linear programming relaxation, NMR spectroscopy, Resonance assignment problem, Shortest path problem",

author = "Bravo-Ferreira, {Jos{\'e} F.S.} and David Cowburn and Yuehaw Khoo and Amit Singer",

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AU - Cowburn, David

AU - Khoo, Yuehaw

AU - Singer, Amit

PY - 2022/5

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N2 - Nuclear Magnetic Resonance (NMR) Spectroscopy is the second most used technique (after X-ray crystallography) for structural determination of proteins. A computational challenge in this technique involves solving a discrete optimization problem that assigns the resonance frequency to each atom in the protein. This paper introduces LIAN (LInear programming Assignment for NMR), a novel linear programming formulation of the problem which yields state-of-the-art results in simulated and experimental datasets.

AB - Nuclear Magnetic Resonance (NMR) Spectroscopy is the second most used technique (after X-ray crystallography) for structural determination of proteins. A computational challenge in this technique involves solving a discrete optimization problem that assigns the resonance frequency to each atom in the protein. This paper introduces LIAN (LInear programming Assignment for NMR), a novel linear programming formulation of the problem which yields state-of-the-art results in simulated and experimental datasets.

KW - Linear programming relaxation

KW - NMR spectroscopy

KW - Resonance assignment problem

KW - Shortest path problem

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NMR assignment through linear programming

Abstract

Keywords

ASJC Scopus subject areas

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