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 |
| Link |
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| 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 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 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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