ArchDB 2014: Structural classification of loops in proteins

Jaume Bonet, Joan Planas-Iglesias, Javier Garcia-Garcia, Manuel A. Marín-López, Narcis Fernandez-Fuentes, Baldo Oliva

Allbwn ymchwil: Cyfraniad at gyfnodolynErthygladolygiad gan gymheiriaid

116 Wedi eu Llwytho i Lawr (Pure)


The function of a protein is determined by its three-dimensional structure, which is formed by regular (i.e. β-strands and α-helices) and non-periodic structural units such as loops. Compared to regular structural elements, non-periodic, non-repetitive conformational units enclose a much higher degree of variability—raising difficulties in the identification of regularities, and yet represent an important part of the structure of a protein. Indeed, loops often play a pivotal role in the function of a protein and different aspects of protein folding and dynamics. Therefore, the structural classification of protein loops is an important subject with clear applications in homology modelling, protein structure prediction, protein design (e.g. enzyme design and catalytic loops) and function prediction. ArchDB, the database presented here (freely available at, represents such a resource and has been an important asset for the scientific community throughout the years. In this article, we present a completely reworked and updated version of ArchDB. The new version of ArchDB features a novel, fast and user-friendly web-based interface, and a novel graph-based, computationally efficient, clustering algorithm. The current version of ArchDB classifies 149,134 loops in 5739 classes and 9608 subclasses.
Iaith wreiddiolSaesneg
Tudalennau (o-i)D315-D319
Nifer y tudalennau5
CyfnodolynNucleic Acids Research
Rhif cyhoeddiD1
Dyddiad ar-lein cynnar20 Tach 2013
Dynodwyr Gwrthrych Digidol (DOIs)
StatwsCyhoeddwyd - 01 Ion 2014

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