Name
Abstract | ||
|---|---|---|
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. |
Year | DOI | Venue |
|---|---|---|
2011 | 10.5591/978-1-57735-516-8/IJCAI11-431 | IJCAI |
Keywords | Field | DocType |
Exploring protein fragment assembly,additional knowledge,Assembling fragment,novel approach,complete conformation,known protein structure,side chain centroid protein,fragments assembly,protein representation,Constraint Logic Programming,energy model | Computer science,Algorithm,Constraint satisfaction problem,Theoretical computer science,Protein Fragment,Preprocessor,Constraint logic programming,Centroid,Protein structure | Conference |
Citations | PageRank | References |
9 | 0.48 | 7 |
Authors | ||
4 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Alessandro Dal Palù | 1 | 211 | 14.97 |
| Agostino Dovier | 2 | 972 | 81.11 |
| Federico Fogolari | 3 | 150 | 10.83 |
| Enrico Pontelli | 4 | 1901 | 181.26 |