Complexity of finding embeddings in a k-tree
SIAM Journal on Algebraic and Discrete Methods
On the Approximation of Shortest Common Supersequencesand Longest Common Subsequences
SIAM Journal on Computing
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)
Efficient Approximation for Triangulation of Minimum Treewidth
UAI '01 Proceedings of the 17th Conference in Uncertainty in Artificial Intelligence
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
Graph algorithms for biological systems analysis
Proceedings of the nineteenth annual ACM-SIAM symposium on Discrete algorithms
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
Stochastic local search for the optimization of secondary structure packing in proteins
LION'10 Proceedings of the 4th international conference on Learning and intelligent optimization
RECOMB'11 Proceedings of the 15th Annual international conference on Research in computational molecular biology
Residues with Similar Hexagon Neighborhoods Share Similar Side-Chain Conformations
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Bidimensionality and geometric graphs
Proceedings of the twenty-third annual ACM-SIAM symposium on Discrete Algorithms
EvoBIO'10 Proceedings of the 8th European conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics
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
P-Binder: a system for the protein-protein binding sites identification
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
Detecting protein conformational changes in interactions via scaling known structures
RECOMB'13 Proceedings of the 17th international conference on Research in Computational Molecular Biology
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This article studies the protein side-chain packing problem using the tree-decomposition of a protein structure. To obtain fast and accurate protein side-chain packing, protein structures are modeled using a geometric neighborhood graph, which can be easily decomposed into smaller blocks. Therefore, the side-chain assignment of the whole protein can be assembled from the assignment of the small blocks. Although we will show that the side-chain packing problem is still NP-hard, we can achieve a tree-decomposition-based globally optimal algorithm with time complexity of O(Nnrottw + 1) and several polynomial-time approximation schemes (PTAS), where N is the number of residues contained in the protein, nrot the average number of rotamers for each residue, and tw = O(N2/3 log N) the treewidth of the protein structure graph. Experimental results indicate that after Goldstein dead-end elimination is conducted, nrot is very small and tw is equal to 3 or 4 most of the time. Based on the globally optimal algorithm, we developed a protein side-chain assignment program TreePack, which runs up to 90 times faster than SCWRL 3.0, a widely-used side-chain packing program, on some large test proteins in the SCWRL benchmark database and an average of five times faster on all the test proteins in this database. There are also some real-world instances that TreePack can solve but that SCWRL 3.0 cannot. The TreePack program is available at http://ttic.uchicago.edu/~jinbo/TreePack.htm.