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Nucleic Acids Research Advance Access published online on November 5, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm953
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© 2007 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

CyBase: a database of cyclic protein sequences and structures, with applications in protein discovery and engineering

Conan K. L. Wang1, Quentin Kaas1, Laurent Chiche2 and David J. Craik1,*

1Institute for Molecular Bioscience, Australian Research Council Special Research, Centre for Functional and Applied Genomics, University of Queensland, Brisbane, Queensland, 4072, Australia and 2Université de Montpellier, CNRS, UMR5048, Centre de Biochimie Structurale, 34090 Montpellier, 3INSERM, U554, Montpellier, France

*To whom correspondence should be addressed. Tel: +61 7 3346 2019; Fax: +61 7 3346 2029; Email: d.craik{at}imb.uq.edu.au

Received September 14, 2007. Revised October 15, 2007. Accepted October 16, 2007.

CyBase was originally developed as a database for backbone-cyclized proteins, providing search and display capabilities for sequence, structure and function data. Cyclic proteins are interesting because, compared to conventional proteins, they have increased stability and enhanced binding affinity and therefore can potentially be developed as protein drugs. The new CyBase release features a redesigned interface and internal architecture to improve user-interactivity, collates double the amount of data compared to the initial release, and hosts a novel suite of tools that are useful for the visualization, characterization and engineering of cyclic proteins. These tools comprise sequence/structure 2D representations, a summary of grafting and mutation studies of synthetic analogues, a study of N- to C-terminal distances in known protein structures and a structural modelling tool to predict the best linker length to cyclize a protein. These updates are useful because they have the potential to help accelerate the discovery of naturally occurring cyclic proteins and the engineering of cyclic protein drugs. The new release of CyBase is available at http://research1t.imb.uq.edu.au/cybase


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