SEQATOMS -- a web tool for identifying missing regions in PDB in sequence context

What you can do:
Visualize all "missing" protein regions in PDB.
  • With over 46 000 proteins, the Protein Data Bank (PDB) is the most important database with structural information of biological macromolecules. PDB files contain sequence and coordinate information.
  • Residues present in the sequence can be absent from the coordinate section, which means their position in space is unknown.
  • Similarity searches are routinely carried out against sequences taken from PDB SEQRES. However, there no distinction is made between residues that have a known or unknown position in the 3D protein structure.
  • We present a FASTA sequence database that is produced by combining the sequence and coordinate information.
  • All residues absent from the PDB coordinate section are masked with lower-case letters, thereby providing a view of these residues in the context of the entire protein sequence, which facilitates inspecting 'missing' regions.
  • We also provide a masked version of the CATH domain database.
  • A user-friendly BLAST interface is available for similarity searching.
  • In contrast to standard (stand-alone) BLAST output, which only contains upper-case letters, our output retains the lower-case letters of the masked regions.
  • Thus, our server can be used to perform BLAST searching case-sensitively.
  • Here, we have applied it to the study of missing regions in their sequence context.
  • PDB
  • protein data bank
  • sequence similarity
  • missing protein regions
  • protein sequence
  • protein coordinate
  • similarity searching
This record last updated: 07-24-2008
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