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Computational Protein Design as a Cost Function Network Optimization Problem

  • Conference paper
Principles and Practice of Constraint Programming (CP 2012)

Part of the book series: Lecture Notes in Computer Science ((LNPSE,volume 7514))

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 different 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.

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Author information

Authors and Affiliations

  1. UBIA, UR 875, INRA, F-31320, Castanet Tolosan, France

    David Allouche, Simon de Givry, George Katsirelos & Thomas Schiex

  2. UMR INRA 792/CNRS 5504, LISBP, INSA, F-31400, Toulouse, France

    Seydou Traoré, Isabelle André & Sophie Barbe

Authors
  1. David Allouche
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  2. Seydou Traoré
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  3. Isabelle André
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  4. Simon de Givry
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  5. George Katsirelos
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  6. Sophie Barbe
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  7. Thomas Schiex
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Editor information

Editors and Affiliations

  1. DEIS Universitá di Bologna, V.le Risorgimento, 2, 40136, Bologna, Italy

    Michela Milano

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Allouche, D. et al. (2012). Computational Protein Design as a Cost Function Network Optimization Problem. In: Milano, M. (eds) Principles and Practice of Constraint Programming. CP 2012. Lecture Notes in Computer Science, vol 7514. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-33558-7_60

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  • DOI: https://doi.org/10.1007/978-3-642-33558-7_60

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-33557-0

  • Online ISBN: 978-3-642-33558-7

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