An integer programming model for protein structure prediction using the 3D-HP side chain model
type: Item
instance of: scholarly article
title: An integer programming model for protein structure prediction using the 3D-HP side chain model
zbMATH Open document ID: 1336.92063
author: Luiz Fernando Nunes
author: Lauro Cesar Galvão
author: Heitor Silvério Lopes
author: Pablo Moscato
author: Regina E. Berretta
published in: Discrete Applied Mathematics
publication date: 2015-12-07T00:00:00Z
review text: In this paper the authors focus on discrete models with side chains and propose an integer programming approach for the 3D-HP side chain protein structure problem. Following an introduction of the prediction problem and an overview of discrete and continuous models proposed for the analysis of the folding process, the authors present in detail the 3D-HP-SC integer programming formulation. First, the mathematical notation is introduced. Next, the accepted interactions between backbones and hydrophilic and hydrophobic side chains are presented. In the next sections, the variables and formulations are described in detail. The paper concludes with an overview of the computational experiments conducted on the ILOG CPLEX optimisation package (details on runtimes and resources are also included). For several instances, previously described in the literature, the optimal solution is reached, using this programming approach.
reviewed by: Irina Ioana Mohorianu
Mathematics Subject Classification ID: 92D20
Mathematics Subject Classification ID: 90C10
zbMATH DE Number: 6516934
zbMATH Keywords: integer programming
zbMATH Keywords: protein folding
zbMATH Keywords: lattice models
zbMATH Keywords: bioinformatics
describes a project that uses: CPLEX
MaRDI profile type: Publication
full work available at URL: j.dam.2015.06.021
OpenAlex ID: W785937070
cites work: Long proteins with unique optimal foldings in the H-P model
cites work: Complexity of protein folding
cites work: Folding in lattice models with side chains
cites work: Finding the lowest free energy conformation of a protein is an NP-hard problem: Proof and implications
DOI: 10.1016/J.DAM.2015.06.021
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description: scientific article; zbMATH DE number 6516934