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Nucleic Acids Research Advance Access published online on October 2, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn599
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

JAIL: a structure-based interface library for macromolecules

Stefan Günther1, Joachim von Eichborn1, Patrick May2 and Robert Preissner1,*

1Institute of Molecular Biology and Bioinformatics, Charité-University Medicine Berlin, Arnimallee 22, 14195 Berlin and 2Max-Planck-Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany

*To whom correspondence should be addressed. Tel: +49-30-8445-1649; Fax: +49-30-8445-1551; Email: robert.preissner{at}charite.de

Received August 20, 2008. Accepted September 4, 2008.

The increasing number of solved macromolecules provides a solid number of 3D interfaces, if all types of molecular contacts are being considered. JAIL annotates three different kinds of macromolecular interfaces, those between interacting protein domains, interfaces of different protein chains and interfaces between proteins and nucleic acids. This results in a total number of about 184 000 database entries. All the interfaces can easily be identified by a detailed search form or by a hierarchical tree that describes the protein domain architectures classified by the SCOP database. Visual inspection of the interfaces is possible via an interactive protein viewer. Furthermore, large scale analyses are supported by an implemented sequential and by a structural clustering. Similar interfaces as well as non-redundant interfaces can be easily picked out. Additionally, the sequential conservation of binding sites was also included in the database and is retrievable via Jmol. A comprehensive download section allows the composition of representative data sets with user defined parameters. The huge data set in combination with various search options allow a comprehensive view on all interfaces between macromolecules included in the Protein Data Bank (PDB). The download of the data sets supports numerous further investigations in macromolecular recognition. JAIL is publicly available at http://bioinformatics.charite.de/jail.


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