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Sequence search

Searches protein and nucleic acid sequences using the mmseqs2 method. The method finds similar protein or nucleic acid chains in the PDB. Mmseqs2 is similar to the well-known BLAST method, but achieves better performance at comparable levels of sensitivity. See the corresponding publication for more details.

Sequences can be searched in two ways:


Note: sequences must be at least 20 residues long. For shorter sequences try the Sequence Motif Search.

The E value, or Expect value, is a parameter that describes the number of hits one can expect to see just by chance when searching a database of a particular size. For example, an E value of 1 indicates that a result will contain one sequence with similar score simply by chance. The scoring takes chain length into consideration and therefore shorter sequences can have identical matches with high E value.

The Sequence Identity Cutoff (%) filter removes the entries of low sequence similarity. The cutoff value is a percentage value between 0 to 100.