ParSe: predict phase-separating protein regions from the primary sequence

This is a form that allows you to enter a sequence and predict the regions in a protein that are disordered, and which subset of those regions can undergo liquid-liquid phase separation (LLPS).

ParSe has been updated. To use version 2, please visit our other site.

Description

Proteins that undergo LLPS have been implicated in the formation of membraneless organelles and are of interest because of their role in regulating the formation of P bodies, the nucleolus, and stress granules. LLPS in intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDRs) is thought to be mediated by many weak, multi-valent, intermolecular interactions.

This algorithm explores the possibility that LLPS can be predicted using two factors. First, the strength of interactions between the protein and solvent, as estimated by a model of the polymer scaling exponent (ν_model). Second, the propensity for a sequence to form β-turns. Using these factors, any protein sequence can be parsed into one of three categories:

• P Regions (P) are intrinsically disordered and prone to undergo LLPS.
• D Regions (D) are intrinsically disordered but do not undergo LLPS.
• F Regions (F) may or may not be intrinsically disordered, but can fold to a stable conformation.

Reference

1. Paiz, E.A., Allen, J.H., Correia, J.J., Fitzkee, N.C., Hough, L.E., Whitten, S.T. “Beta turn propensity and a model polymer scaling exponent identify intrinsically disordered phase-separating proteins” J. Biol. Chem. 297, 101343 (2021). https://doi.org/10.1016/j.jbc.2021.101343

Sequence length: 
Whole sequence νmodel: 
Whole sequence β-turn propensity: 
Whole sequence rmodel: