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Computational Protein Design: trying an Answer Set Programming approach to solve the problem

Hugo Bazille 1 Jacques Nicolas 2, *
* Corresponding author
2 Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
Abstract : Proteins are macromolecules made of a chain of amino-acids. The combinatorial nature of the space of possible protein conformations makes computer-aided protein study a major research field in bioinformatics. The problem of \textit{computational protein design} aims at finding the best protein conformation to perform a given task. This problem can be reduced to an optimization problem, looking for the minimum of an energy function depending on the amino-acid interactions in the protein. We have designed a model based on Answer Set Programming. The CPD problem may be easily modeled as an ASP program but a practical implementation able to work on real-sized instances has never been published. We have raised the main source of difficulty for current ASP solvers and ran a series of benchmarks highlighting the importance of finding a good upper bound estimation of the target minimum energy to reduce the amount of combinatorial search. Our solution clearly outperforms a direct ASP implementation without this estimation and has comparable performances with respect to SAT-based approaches. It remains less efficient that the recent approach by cost function networks of D. Allouche & al., showing there exists still some place for improving the optimization component in ASP with more dynamical strategies.
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https://hal.inria.fr/hal-01063030
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Submitted on : Friday, September 12, 2014 - 2:17:28 PM
Last modification on : Friday, July 10, 2020 - 4:16:08 PM
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Hugo Bazille, Jacques Nicolas. Computational Protein Design: trying an Answer Set Programming approach to solve the problem. 10th Workshop on Constraint-Based Methods for Bioinformatics (WCB'14), Nicos Angelopoulos (Imperial College, UK) Simon de Givry (MIAT-INRA, France), Sep 2014, Lyon, France. ⟨hal-01063030⟩

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