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CLP-based protein fragment assembly*

Published online by Cambridge University Press:  09 July 2010

ALESSANDRO DAL PALÙ ,
AGOSTINO DOVIER ,
FEDERICO FOGOLARI  and
ENRICO PONTELLI
ALESSANDRO DAL PALÙ
Affiliation:
Department of Mathematics, University of Parma, Italy
AGOSTINO DOVIER
Affiliation:
Department of Mathematics and Computer Science, University of Udine, Italy
FEDERICO FOGOLARI
Affiliation:
Department of Biomedical Sciences, University of Udine, Italy
ENRICO PONTELLI
Affiliation:
Department of Computer Science, New Mexico State University, NM, USA
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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.

Keywords

constraint logic programmingprotein fragment assembly
Type
Regular Papers
Information
Theory and Practice of Logic Programming , Volume 10 , Special Issue 4-6: 26th International Conference on Logic Programming , July 2010 , pp. 709 - 724
Copyright
Copyright © Cambridge University Press 2010

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