A tree-decomposition approach to protein structure prediction

This paper proposes a tree decomposition of protein structures, which can be used to efficiently solve two key subproblems of protein structure prediction: protein threading for backbone prediction and protein side-chain prediction. To develop a unified tree-decomposition based approach to these two subproblems, we model them as a geometric neighborhood graph labeling problem. Theoretically, we can have a low-degree polynomial time algorithm to decompose a geometric neighborhood graph G=(V,E) into components with size O(|V|/sup 2/spl bsol/3/ log|V|). The computational complexity of the tree-decomposition based graph labeling algorithms is O(|V|/spl Delta//sup tw+1/]) where /spl Delta/ is the average number of possible labels for each vertex and tw(=O(|V|/sup 2/3/ log|V|)) the tree width of G. Empirically, tw is very small and the tree-decomposition method can solve these two problems very efficiently. This paper also compares the computational efficiency of the tree-decomposition approach with the linear programming approach to these two problems and identifies the condition under which the tree-decomposition approach is more efficient than the linear programming approach. Experimental result indicates that the tree-decomposition approach is more efficient most of the time.

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