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

Research output: Contribution to journalArticlepeer-review

32 Citations (SciVal)
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Abstract

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 http://sbi.imim.es/archdb), 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.
Original languageEnglish
Pages (from-to)D315-D319
Number of pages5
JournalNucleic Acids Research
Volume42
Issue numberD1
Early online date20 Nov 2013
DOIs
Publication statusPublished - 01 Jan 2014

Keywords

  • Cluster Analysis
  • Databases, Protein
  • Internet
  • Protein Structure, Secondary
  • Proteins/classification

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