A constraint programming approach to bioinformatics structural problems

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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.
Original languageUnknown
Title of host publicationLECTURE NOTES IN COMPUTER SCIENCE
Pages33--49
Volume4354
Publication statusPublished - 1 Jan 2007
Event9th International Symposium on Practical Aspects of Declarative Languages -
Duration: 1 Jan 2007 → …

Conference

Conference9th International Symposium on Practical Aspects of Declarative Languages
Period1/01/07 → …

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