Complexity of finding embeddings in a k-tree
SIAM Journal on Algebraic and Discrete Methods
Separators for sphere-packings and nearest neighbor graphs
Journal of the ACM (JACM)
An optimal algorithm for approximate nearest neighbor searching fixed dimensions
Journal of the ACM (JACM)
On the approximation of protein threading
Theoretical Computer Science - Special issue: Genome informatics
Side Chain-Positioning as an Integer Programming Problem
WABI '01 Proceedings of the First International Workshop on Algorithms in Bioinformatics
Protein side-chain packing problem: a maximum edge-weight clique algorithmic approach
APBC '04 Proceedings of the second conference on Asia-Pacific bioinformatics - Volume 29
A Semidefinite Programming Approach to Side Chain Positioning with New Rounding Strategies
INFORMS Journal on Computing
Efficient approximation for triangulation of minimum treewidth
UAI'01 Proceedings of the Seventeenth conference on Uncertainty in artificial intelligence
A Tree-Decomposition Approach to Protein Structure Prediction
CSB '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference
Efficient Parameterized Algorithms for Biopolymer Structure-Sequence Alignment
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Graph algorithms for biological systems analysis
Proceedings of the nineteenth annual ACM-SIAM symposium on Discrete algorithms
Free energy estimates of all-atom protein structures using generalized belief propagation
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
Rapid and accurate protein side chain prediction with local backbone information
RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology
Protein side-chain placement through MAP estimation and problem-size reduction
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Efficient parameterized algorithm for biopolymer structure-sequence alignment
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
A parameterized algorithm for protein structure alignment
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
LoopWeaver --- loop modeling by the weighted scaling of verified proteins
RECOMB'12 Proceedings of the 16th Annual international conference on Research in Computational Molecular Biology
How accurately can we model protein structures with dihedral angles?
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
Protein structure optimization by side-chain positioning via beta-complex
Journal of Global Optimization
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This paper proposes a novel tree decomposition based side-chain assignment algorithm, which can obtain the globally optimal solution of the side-chain packing problem very efficiently. Theoretically, the computational complexity of this algorithm is O((N + M)n$_{rot}^{tw + 1}$) where N is the number of residues in the protein, M the number of interacting residue pairs, nrot the average number of rotamers for each residue and $O((N + M)n^{tw+1}_{rot})$ the tree width of the residue interaction graph. Based on this algorithm, we have developed a side-chain prediction program SCATD (Side Chain Assignment via Tree Decomposition). Experimental results show that after the Goldstein DEE is conducted, nrot is around 3.5, tw is only 3 or 4 for most of the test proteins in the SCWRL benchmark and less than 10 for all the test proteins. SCATD runs up to 90 times faster than SCWRL 3.0 on some large proteins in the SCWRL benchmark and achieves an average of five times faster speed on all the test proteins. If only the post-DEE stage is taken into consideration, then our tree-decomposition based energy minimization algorithm is more than 200 times faster than that in SCWRL 3.0 on some large proteins. SCATD is freely available for academic research upon request.