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PMID: 17986451 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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

Nucleic acids research ·Vol. 36 ·No. Database issue ·2008-01-00 ·Pages D206-10

Wang CK, Kaas Q, Chiche L, Craik DJ

Abstract

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.

MeSH Terms
Bacterial Proteins/chemistry Computer Graphics Cyclotides/chemistry Databases, Protein Defensins/chemistry Drug Design Internet Protein Conformation Protein Engineering Proteins/chemistry Sequence Analysis, Protein Software Trypsin Inhibitors/chemistry User-Computer Interface
Chemicals
Bacterial Proteins Cyclotides Defensins Proteins Trypsin Inhibitors theta-defensin
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Wang Conan K L
Institute for Molecular Bioscience, Australian Research Council Special Research, Centre for Functional and Applied Genomics, University of Queensland, Brisbane, Queensland, 4072, Australia.
Kaas Quentin
Chiche Laurent
Craik David J
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkm953
Published
2008-01-00
Epub
2007-00-05
Pages
D206-10
Language
English
Region
England
NLM ID
0411011
PMCID
PMC2239000
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkm953 PMC Full Text View journal details
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