Using Constraint Programming and Local Search Methods to Solve Vehicle Routing Problems
CP '98 Proceedings of the 4th International Conference on Principles and Practice of Constraint Programming
Logic Programming Techniques in Protein Structure Determination: Methodologies and Results
LPNMR '09 Proceedings of the 10th International Conference on Logic Programming and Nonmonotonic Reasoning
International Journal of Data Mining and Bioinformatics
Clp-based protein fragment assembly*
Theory and Practice of Logic Programming
A filtering technique for fragment assembly- based proteins loop modeling with constraints
CP'12 Proceedings of the 18th international conference on Principles and Practice of Constraint Programming
A constraint solver for flexible protein models
Journal of Artificial Intelligence Research
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The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict potential 3D conformations of a protein via fragments assembly. The fragments are extracted and clustered by a preprocessor from a database of known protein structures. Assembling fragments into a complete conformation is modeled as a constraint satisfaction problem solved using CLP. The approach makes use of a simplified Cα-side chain centroid protein model, that offers efficiency and a good approximation for space filling. The approach adapts existing energy models for protein representation and applies a large neighboring search (LNS) strategy. The results show the feasibility and efficiency of the method, and the declarative nature of the approach simplifies the introduction of additional knowledge and variations of the model.