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A Constraint Programming Approach to Bioinformatics Structural Problems

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Practical Aspects of Declarative Languages (PADL 2007)

Part of the book series: Lecture Notes in Computer Science ((LNPSE,volume 4354))

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Abstract

In this paper we show how Constraint Programming (CP) techniques have been used to handle bioinformatics structural problems, namely in protein structure prediction and protein interaction (docking). Solving these problems requires innovative modelling of the problem variables and constraints, and the application of advanced CP features to handle the problems efficiently, namely the exploitation of global constraints and local search, in addition to more standard binary constraint propagation. Both applications, respectively PSICO (Processing Structural Information with Constraint programming and Optimisation), and BiGGER (Bimolecular complex Generation with Global Evaluation and Ranking) have been incorporated in a platform, Chemera, that aims at supporting (and has effectively supported, namely in protein docking), biochemists in their research.

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Authors and Affiliations

  1. Dep. de Informática, Universidade Nova de Lisboa, 2825 Monte de Caparica, Portugal

    Pedro Barahona & Ludwig Krippahl

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  1. Pedro Barahona
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  2. Ludwig Krippahl
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Editors and Affiliations

  1. Institut für Informatik, CAU Kiel, Germany

    Michael Hanus

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Barahona, P., Krippahl, L. (2006). A Constraint Programming Approach to Bioinformatics Structural Problems. In: Hanus, M. (eds) Practical Aspects of Declarative Languages. PADL 2007. Lecture Notes in Computer Science, vol 4354. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-69611-7_2

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  • DOI: https://doi.org/10.1007/978-3-540-69611-7_2

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-69608-7

  • Online ISBN: 978-3-540-69611-7

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