Skip to Main content Skip to Navigation
Conference papers

Computational protein design as a cost function network optimization problem

Abstract : Proteins are chains of simple molecules called amino acids. The three-dimensional shape of a protein and its amino acid composition define its biological function. Over millions of years, living organisms have evolved and produced a large catalog of proteins. By exploring the space of possible amino-acid sequences, protein engineering aims at similarly designing tailored proteins with specific desirable properties. In Computational Protein Design (CPD), the challenge of identifying a protein that performs a given task is defined as the combinatorial optimization problem of a complex energy function over amino acid sequences. In this paper, we introduce the CPD problem and some of the main approaches that have been used to solve it. We then show how this problem directly reduces to Cost Function Network (CFN) and 0/1LP optimization problems. We construct di erent real CPD instances to evaluate CFN and 0/1LP algorithms as implemented in the toulbar2 and cplex solvers. We observe that CFN algorithms bring important speedups compared to the CPD platform osprey but also to cplex.
Document type :
Conference papers
Complete list of metadatas

Cited literature [36 references]  Display  Hide  Download

https://hal.archives-ouvertes.fr/hal-01191320
Contributor : Archive Ouverte Prodinra <>
Submitted on : Tuesday, September 1, 2015 - 4:44:42 PM
Last modification on : Monday, November 23, 2020 - 12:56:03 PM
Long-term archiving on: : Wednesday, December 2, 2015 - 12:44:48 PM

File

CPD-Final_{D945279E-D10A-4077-...
Files produced by the author(s)

Identifiers

Collections

Citation

David Allouche, Seydou Traore, Isabelle André, Simon de Givry, George Katsirelos, et al.. Computational protein design as a cost function network optimization problem. CP 2012 - 18th International Conference on Principles and Practice of Constraint Programming, Oct 2012, Québec, Canada. pp.10, ⟨10.1007/978-3-642-33558-7_60⟩. ⟨hal-01191320⟩

Share

Metrics

Record views

196

Files downloads

339