The paper describes a constraint-based solution to the protein folding problem on face-centered cubic lattices---a biologically meaningful approximation of the general protein folding problem. The paper improves the results presented in [15] and introduces new ideas for improving efficiency: (i) proper reorganization of the constraint structure; (ii) development of novel, both general and problem-specific, heuristics; (iii) exploitation of parallelism. Globally, we obtain a speed up in the order of 60 w.r.t. [15]. We show how these results can be employed to solve the folding problem for large proteins containing subsequences whose conformation is already known.
Heuristics, Optimizations, and Parallelism for Protein StructurePrediction in CLP(FD) / DAL PALU', Alessandro; A. DOVIER AND E., Pontelli. - (2005), pp. 230-241. (Intervento presentato al convegno 7th ACM SIGPLAN international conference on Principles and practice of declarative programming) [10.1145/1069774.1069796].
Heuristics, Optimizations, and Parallelism for Protein StructurePrediction in CLP(FD).
DAL PALU', Alessandro;
2005-01-01
Abstract
The paper describes a constraint-based solution to the protein folding problem on face-centered cubic lattices---a biologically meaningful approximation of the general protein folding problem. The paper improves the results presented in [15] and introduces new ideas for improving efficiency: (i) proper reorganization of the constraint structure; (ii) development of novel, both general and problem-specific, heuristics; (iii) exploitation of parallelism. Globally, we obtain a speed up in the order of 60 w.r.t. [15]. We show how these results can be employed to solve the folding problem for large proteins containing subsequences whose conformation is already known.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
