title: CyBase: a database of cyclic protein sequences and structures, with applications in protein discovery and engineering.
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.
authors.affiliation: Institute for Molecular Bioscience, Australian Research Council Special Research, Centre for Functional and Applied Genomics, University of Queensland, Brisbane, Queensland, 4072, Australia.
authors.forename: Conan K L
authors.initials: CK
authors.lastname: Wang
authors.forename: Quentin
authors.initials: Q
authors.lastname: Kaas
authors.forename: Laurent
authors.initials: L
authors.lastname: Chiche
authors.forename: David J
authors.initials: DJ
authors.lastname: Craik
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry; D003196:Computer Graphics; D047169:Cyclotides / Q000737:chemistry; D030562:Databases, Protein; D023082:Defensins / Q000737:chemistry; D015195:Drug Design; D020407:Internet; D011487:Protein Conformation; D015202:Protein Engineering; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein; D012984:Software; D014361:Trypsin Inhibitors / Q000737:chemistry; D014584:User-Computer Interface
chemical_list: D001426:Bacterial Proteins; D047169:Cyclotides; D023082:Defensins; D011506:Proteins; D014361:Trypsin Inhibitors; C450142:theta-defensin