ArchDB - Biological DataBase of Protein Loops

ArchDB is a compilation of structural classifications of loops extracted from known protein structures. Loops in ArchDB have been classified using an improved version (Espadaler et al.) of the original ArchType program published in 1997 by Oliva et al..

ArchDB includes 4 classifications:

ArchDB40 contains the classification of loops extracted from proteins domains of ASTRAL SCOP with less that 40% sequence identity.
ArchDB95 contains the classification of loops extracted from proteins domains of ASTRAL SCOP with less that 95% sequence identity.
ArchDB-EC is a classification of loops extracted from proteins with known enzymatic function
ArchDB-KI is a curated classification database of kinase loops EC number 2.7.X.X with functional information of residues.

ArchDB40 last updated on 12-06-2007: 27635 classified loops
ArchDB95 last updated on 13-06-2007: 41294 classified loops
ArchDB-EC last updated on 23-03-2005: 23487 classified loops
ArchDB-KI last updated on 23-05-2004 : 2755 classified loops

Oliva B, Bates PA, Querol E, Aviles FX, Sternberg MJ. An automated classification of the structure of protein loops.J Mol Biol. 1997 Mar 7;266(4):814-30.

Oliva B, Bates PA, Querol E, Aviles FX, Sternberg MJ. Automated classification of antibody complementarity determining region 3 of the heavy chain (H3) loops into canonical forms and its application to protein structure prediction. J Mol Biol. 1998 Jun 26;279(5):1193-210.

Espadaler J, Fernandez-Fuentes N, Hermoso A, Querol E, Aviles FX , Sternberg M, Oliva B. ArchDB: Automated protein loop classification as a tool for Structural Genomics. Nucl Acids Res. 2004 Jan 1;32: DataBase Issue D185-8.

Fernandez-Fuentes N, Hermoso A, Espadaler J, Querol E, Aviles FX, Oliva B. Classification of common functional loops of kinase super-families. Proteins. 2004 Aug 15;56(3):539-55.