New Features

Sequence Motif Searching


Use Advanced Search to find short sequence patterns in PDB structure FASTA sequences using the following syntax options:

  • Simple: Sequence fragments using IUPAC one-letter codes for amino acids (e.g., MQTIF) plus ‘X’ to indicate any amino acid at a position. For example, use XPPXP to search for SH3 domains (where X is a variable residue and P is Proline)
  • PROSITE: Complex queries that include ambiguities, exempt amino acids, repetition, and/or positioning at N- or C-terminus can be expressed using PROSITE patterns (e.g., [AC]-x-V-x(4)-{ED}). Visit PROSITE for definitions
  • Regex: Build complex sequence searches using regular expressions (Details)

Set "Display Results as" to Polymer Entities to view the numbering for the sequential sequence match region (corresponding to PDBx/mmCIF file numbering).

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