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Seminar Details

Date 2-12-2010
Time 12:00
Room/Location Sala Conferenze
Title CLP-based protein fragment assembly
Speaker Agostino Dovier
Affiliation Universita' di Udine
Abstract In the talk it will be presented 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 preprocessoró also developed for this workó 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 CA-side chain centroid protein model that offers efficiency and a good approximation for space filling. The approach adapts existing energy models to the protein representation used and applies a large neighboring search strategy. The results show 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.
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