Fast protein folding in the hydrophobic-hydrophilic model within three-eights of optimal
STOC '95 Proceedings of the twenty-seventh annual ACM symposium on Theory of computing
Protein folding in the hydrophobic-hydrophilic (HP) is NP-complete
RECOMB '98 Proceedings of the second annual international conference on Computational molecular biology
On the complexity of protein folding (abstract)
RECOMB '98 Proceedings of the second annual international conference on Computational molecular biology
Tree adjoining grammars for RNA structure prediction
Theoretical Computer Science - Special issue: Genome informatics
SODA '97 Proceedings of the eighth annual ACM-SIAM symposium on Discrete algorithms
Approximation algorithms for protein folding prediction
Proceedings of the tenth annual ACM-SIAM symposium on Discrete algorithms
Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots
Discrete Applied Mathematics - Special volume on combinatorial molecular biology
A new algorithm for protein folding in the HP model
SODA '02 Proceedings of the thirteenth annual ACM-SIAM symposium on Discrete algorithms
A complete and effective move set for simplified protein folding
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
RNA secondary structure prediction with simple pseudoknots
APBC '04 Proceedings of the second conference on Asia-Pacific bioinformatics - Volume 29
On the computational complexity of 2-interval pattern matching problems
Theoretical Computer Science
Approximating the 2-interval pattern problem
ESA'05 Proceedings of the 13th annual European conference on Algorithms
Improved Approximation Algorithms for Predicting RNA Secondary Structures with Arbitrary Pseudoknots
AAIM '07 Proceedings of the 3rd international conference on Algorithmic Aspects in Information and Management
Approximation Algorithms for Predicting RNA Secondary Structures with Arbitrary Pseudoknots
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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The lattice approach to biological structural analysis was made popular by the HP model for protein folding, but had not been used previously for RNA secondary structure prediction.We introduce the Delta toolset for the structural analysis of biological sequences on a 3D triangular lattice. The Delta toolset includes a proof-of-concept RNA folding program that is both fast and accurate in predicting the secondary structures with pseudoknots of short RNA sequences.