Heuristics, optimizations, and parallelism for protein structure prediction in CLP(FD)

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. Categories and Subject Descriptors J.3 [Computer Applications]: LIFE AND MEDICAL SCIENCES General Terms Algorithms,Experimentations Keywords Constraint logic programming, parallelism, bioinformatics

• Type: Conference
• Year: 2005
• Where: PPDP
• Authors: Alessandro Dal Palù, Agostino Dovier, Enrico Pontelli
• Keywords: Folding Problem, General Protein Folding, PPDP 2005, Protein Folding Problem