LOCALCIDER

Classification of Intrinsically Disordered Ensemble Regions - localCIDER


Synopsis

Calculates and presents various sequence parameters associated with disordered protein sequences

Description

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]
  • Das-Pappu phase diagram position: Where on the Das-Pappu phase diagram (fraction of positive charge vs. fraction of negative charge) does the sequence fall
CIDER is actually a Web Service which calls the program localCIDER on the web-server. In NMRbox, localCIDER is a Python package installed locally which can perform all the analysis CIDER provides and more.

URL

http://pappulab.wustl.edu/CIDER/

Versions

NMRbox Version Software Version
3.0.0 0.1.14,

Keywords

  • Utilities
  • Intrinsically Disordered Proteins (IDPs)