ArchDB: automated protein loop classification as a tool for structural genomics

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D185-8. doi: 10.1093/nar/gkh002.


The annotation of protein function has become a crucial problem with the advent of sequence and structural genomics initiatives. A large body of evidence suggests that protein structural information is frequently encoded in local sequences, and that folds are mainly made up of a number of simple local units of super-secondary structural motifs, consisting of a few secondary structures and their connecting loops. Moreover, protein loops play an important role in protein function. Here we present ArchDB, a classification database of structural motifs, consisting of one loop plus its bracing secondary structures. ArchDB currently contains 12,665 super-secondary elements classified into 1496 motif subclasses. The database provides an easy way to retrieve functional information from protein structures sharing a common motif, to search motifs found in a given SCOP family, superfamily or fold, or to search by keywords on proteins with classified loops. The ArchDB database of loops is located at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Animals
  • Automation
  • Computational Biology
  • Databases, Protein*
  • Genomics*
  • Humans
  • Internet
  • Molecular Sequence Data
  • Protein Structure, Secondary
  • Proteins / chemistry*
  • Proteins / classification*
  • Proteins / metabolism


  • Proteins