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PAST is a new web service providing fast structural queries of the Protein Data Bank. The search engine is based on an adaptation of the generalized suffix tree and relies on a translation- and rotation-invariant representation of the protein backbone. The search procedure is completely independent of the amino acid sequence of the polypeptide chains. The(More)
The main contribution of this paper is a novel approach for fast searching in huge structural databases like the PDB. The data structure is based on an adap-tion of the generalized suffix tree and relies on an translation-and rotation-invariant representation of the protein backbone. The method was evaluated by applying structural queries to the PDB and(More)
Preface I am deeply grateful to all which have contributed to this work by their comments and discussions, by hints, advice, and patience. In particular, I would like to thank For allowing me to present joint work here, many thanks are due to my coauthors and colleagues The algorithms group (" LEA ") at the Technische Universität München has always provided(More)
We use a dynamic variant for the iterative application of the Brandes Algorithm. In each iteration only one node is removed and, on average, large parts of the shortest paths graphs do not need to be recomputed. Our algorithm uses this observation to restrict the necessary re-computations to the affected nodes-an approach that is employed by a whole class(More)
This work considers the (lowest) common ancestor problem in weighted directed acyclic graphs. The minimum-weight (lowest) common ancestor of two vertices is the vertex among the set of (lowest) common ancestors with the smallest ancestral distance. For the all-pairs minimum-weight common ancestor problem we present an O(nm) algorithm for arbitrary edge(More)
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