NMR assignment through linear programming

DOI10.1007/S10898-021-01004-3MaRDI QIDQ2131136zbMATH OpenOpenAlexFDO

Authors David Cowburn, Yuehaw Khoo, A. Singer, José F. S. Bravo Ferreira

Publication date 25 April 2022

Published in Journal of Global Optimization (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/2008.03641

zbMATH Keywords

linear programming relaxationNMR spectroscopyresonance assignment problemshortest path problem

Mathematics Subject Classification ID

Discrete location and assignment (90B80) Linear programming (90C05) Integer programming (90C10)

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.

Recommendations

• Model-Based Assignment and Inference of Protein Backbone Nuclear Magnetic Resonances
• Developing a scoring function for NMR structure-based assignments using machine learning
• Progress in nuclear vector replacement for NMR protein structure-based assignments
• Algorithms and analytic solutions using sparse residual dipolar couplings for high-resolution automated protein backbone structure determination by NMR
• Mathematical aspects of protein structure determination with NMR orientational restraints

Cites work

• scientific article; zbMATH DE number 1764950 (Why is no real title available?)
• Network flows. Theory, algorithms, and applications.
• Semidefinite programming approach for the quadratic assignment problem with a sparse graph

Cited in

(5)

• Optimal pathway reconstruction on 3D NMR maps
• Mathematical aspects of protein structure determination with NMR orientational restraints
• Progress in nuclear vector replacement for NMR protein structure-based assignments
• Developing a scoring function for NMR structure-based assignments using machine learning
• scientific article; zbMATH DE number 5254799 (Why is no real title available?)

Describes a project that uses

Uses Software

• BioMagResBank
• Gurobi
• ARIAweb
• CYANA

This page was built for publication: NMR assignment through linear programming

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2131136)