Welcome to CyBase

This site is dedicated to the study of a fascinating new class of proteins that possess a cyclic backbone in which the N and C termini have been joined with a conventional amide bond. These recently characterised molecules have now been found in organisms from all kingdoms of life and given the current rate of discovery the number of sequences could soon number in the hundreds.

Research in our lab is aimed at further characterising cyclic proteins and adapting them for commercial and medicinal use. In particular we work on a class of cyclic protein named the cyclotides. These proteins are found in the plants of the Rubiaceae and Violaceae and our specific goals include: determining the role that cyclotides play in plants, discovering the mechanism of action of the wide range of biological activities displayed by the cyclotides (including anti-HIV, anti-bacterial and insecticidal activity), characterising the genetics of the cyclotides and further discovery of novel cyclotides.

In order to track the rapidly increasing number of cyclic peptides that have been characterised this website presents a database of cyclic protein sequences and structures.

Cyclic peptide examples

Cyclic peptides have been found in a range of organisms including the cyclotides from plants, RTD-1 from macaque monkeys and AS-48 from bacteria.

News: A new method called CyPred has been developed at the University of Alberta in the laboratory of Lukasz Kurgan to predict if a protein is cyclic from its protein sequence.
Kedarisetti P., Mizianty MJ, Kaas Q., Craik D.J., and Kurgan L. Prediction and characterization of cyclic proteins from sequences in three domains of life. BBA - Proteins and Proteomic (2013) In Press.
News: A page now describes the collection of plants that have been screened for cyclotides content, whether cyclotides have been found or not. People carrying out cyclotide research are encouraged to submit the name of the plant species that they examined to the website in order to evaluate cyclotide distribution.
Gerlach S.L, Göransson U., Kaas Q., Craik D.J., Mondal D., and Gruber C.W. A systematic approach to document cyclotide distribution in plant species from genomic, transcriptomic and peptidomic analysis. Biopolymers Peptide Science (2013) In Press.

Statistics Table (generated on Tuesday 16th of July 2024)

Number of Entries Species Coverage Links to UniProt, Genbank or PDB
Proteins 1818 178 608
Squash trypsin inhibitor 116 8 17
Primate 14 3 15
PawS-Derived Peptides 3 2 4
Orbitide 219 57 31
Mushroom 4 1 6
Cyclotide 1362 93 509
Cyclised linear proteins 15 1 4
BBI-like trypsin inhibitor 63 7 19
Bacterial 22 12 27
Nucleotides 291 49 221
Structures 83 38 83
Assayed Proteins 250 57 NA

Please cite:

Wang CK, Kaas Q, Chiche L, Craik DJ (2008) CyBase: a database of cyclic protein sequences and structures, with applications in protein discovery and engineering. Nucleic Acids Res. D206-10

Mulvenna JP, Wang C, Craik DJ (2006) CyBase: a database of cyclic protein sequence and structure. Nucleic Acids Res. D192-4