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BACKGROUND: The alignment of protein-protein interaction networks was recently formulated as an integer quadratic programming problem, along with a linearization that can be solved by integer linear programming software tools. However, the resulting integer linear program has a huge number of variables and constraints, rendering it of no practical use. RESULTS: We present a compact integer linear programming reformulation of the protein-protein interaction network alignment problem, which can be solved using state-of-the-art mathematical modeling and integer linear programming software tools, along with empirical results showing that small biological networks, such as virus-host protein-protein interaction networks, can be aligned in a reasonable amount of time on a personal computer and the resulting alignments are structurally coherent and biologically meaningful. CONCLUSIONS: The implementation of the integer linear programming reformulation using current mathematical modeling and integer linear programming software tools provided biologically meaningful alignments of virus-host protein-protein interaction networks.
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10.1186/s12859-020-03733-w
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document_parses/pdf_json/e53430ee925aaef8712548fc9a7d66add71a2ff0.json
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document_parses/pmc_json/PMC7671827.xml.json
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Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks
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