On the complexity of protein folding (extended abstract)
STOC '98 Proceedings of the thirtieth annual ACM symposium on Theory of computing
Applying Constraint Programming to Protein Structure Determination
CP '99 Proceedings of the 5th International Conference on Principles and Practice of Constraint Programming
Opportunities for Combinatorial Optimization in Computational Biology
INFORMS Journal on Computing
Heuristics, optimizations, and parallelism for protein structure prediction in CLP(FD)
PPDP '05 Proceedings of the 7th ACM SIGPLAN international conference on Principles and practice of declarative programming
Principles of Constraint Programming
Principles of Constraint Programming
International Journal of Data Mining and Bioinformatics
CP'07 Proceedings of the 13th international conference on Principles and practice of constraint programming
A constraint solver for flexible protein models
Journal of Artificial Intelligence Research
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The paper describes the formalization and implementation of an efficient constraint programming framework operating on 3D crystal lattices. The framework is motivated and applied to address the problem of solving the ab-initio protein structure prediction problem—i.e., predicting the 3D structure of a protein from its amino acid sequence. Experimental results demonstrate that our novel approach offers up to a 3 orders of magnitude of speedup compared to other constraint-based solutions proposed for the problem at hand.