ABOUT
Classification of Intrinsically Disordered Ensemble Regions (CIDER) allows for the easy calculation and presentation of various sequence parameters associated with disordered protein sequences.
Specifically it allows for the calculation of the following sequence parameters:
- κ (kappa): A measure of the extent of charge segregation in a sequence as defined by Das & Pappu[2]
- FCR: The fraction of charged residues in a sequence
- NCPR: The net charge per residue (can be positive or negative)
- Hydropathy: The mean hydropathy of a sequence, calculated as the average of a 0-9 renormalized Kyte-Doolittle hydrophobicity scale [3]
- Fraction disorder promoting: The fraction of residues which are classified as 'disorder promoting' as defined by Uversky [4]
- Diagram-of-states position: Where on the diagram-of-states (fraction of positive charge vs. fraction of negative charge) does the sequence fall
In addition to these parameters, a sequence annotated diagram-of-states plot is automatically generated. If a single sequence is submitted, the linear net charge per residue (NCPR) and linear hydropathy are also calculated. These data are plotted, and available for download.
If there are other parameters of interest please don't hesitate to contact us to see if these can be incorporated into CIDER or localCIDER's analysis routines.
Usage guidelines
CIDER is meant to provide an easy to use tool for 'quickly checking' sequence parameters. It is not designed for high-throughput analysis. If you're interested in carrying out mass analysis have a look in the help section.
Developers and contact
CIDER was written by Alex Holehouse and James Ahad. Many other people have contributed code, ideas, and discussion, towards its development. CIDER is effectively a web frontend to localCIDER, which was also developed in the Pappu Lab. For more information on localCIDER, please see the link in the top navigation bar (external site). For bug reports, feature requests, or anything else please contact Alex at alex.holehouse@wustl.edu.
Citing CIDER
A manuscript is currently in preparation. For now, please cite analysis done with CIDER or localCIDER using the abstract from the Biophysical Society meetingas follows (if localCIDER was used, please include the version):Holehouse, A.S., Ahad, J., Das, R.K., and Pappu, R.V. (2015). CIDER: Classification of Intrinsically Disordered Ensemble Regions. Biophys. J. 108, 228a.