Clp-based protein fragment assembly*

Authors:
Alessandro Dal palÙ;Agostino Dovier;Federico Fogolari;Enrico Pontelli
Affiliations:
Department of mathematics, university of parma, italy;Department of mathematics and computer science, university of udine, italy;Department of biomedical sciences, university of udine, italy;Department of computer science, new mexico state university, nm, usa
Venue:
Theory and Practice of Logic Programming
Year:
2010

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Abstract

The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments are extracted by a preprocessor—also developed for this work—from a database of known protein structures that clusters and classifies the fragments according to similarity and frequency. The problem of assembling fragments into a complete conformation is mapped to a constraint solving problem and solved using CLP. The constraint-based model uses a medium discretization degree Cα-side chain centroid protein model that offers efficiency and a good approximation for space filling. The approach and adapts existing energy models to the protein representation used and applies a large neighboring search strategy. The results shows the feasibility and efficiency of the method. The declarative nature of the solution allows to include future extensions, e.g., different size fragments for better accuracy.