Detection of common three-dimensional substructures in proteins.

  title={Detection of common three-dimensional substructures in proteins.},
  author={Gert Vriend and Christian Sander},
  volume={11 1},
We present a fully automatic algorithm for three-dimensional alignment of protein structures and for the detection of common substructures and structural repeats. Given two proteins, the algorithm first identifies all pairs of structurally similar fragments and subsequently clusters into larger units pairs of fragments that are compatible in three dimensions. The detection of similar substructures is independent of insertion/deletion penalties and can be chosen to be independent of the topology… CONTINUE READING

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