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Structure Prediction Terminology

  • In order to build a model for an unknown query sequence (also often known as the target sequence) you need to find a relationship with a protein of known structure.
  • These proteins of known structure or “templates” are stored in the only repository for protein structures, the Protein Data Bank (PDB).
  • The most important part of any structure prediction is the alignment between the target and template. Without a good alignment, the rest of the prediction will suffer.
  • The method that is used to find the structural template will always return an alignment, but the alignment should always be checked by hand.