Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks
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 variab...
| Autores: | , , , |
|---|---|
| Formato: | artículo |
| Fecha de publicación: | 2020 |
| País: | España |
| Recursos: | Instituto de Salud Carlos III (ISCIII) |
| Repositorio: | Repisalud |
| Idioma: | inglés |
| OAI Identifier: | oai:repisalud.isciii.es:20.500.12105/22867 |
| Acesso em linha: | https://hdl.handle.net/20.500.12105/22867 |
| Access Level: | acceso abierto |
| Palavra-chave: | Systems biology Virus-host protein-protein interaction Integer linear programming Network alignment Graph matching Modelos Teóricos Algoritmos Programas Informáticos Mapas de Interacción de Proteínas Programación Lineal Software Protein Interaction Maps Programming, Linear Algorithms Models, Theoretical |
| Resumo: | 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. |
|---|