Tools

HPS model

A coarse-grained model for simulating IDP conformations PLOS Comput. Biol. 2018,
with temperature dependent hydropathy (T-HPS) ACS Cent. Sci. 2019,
and salting-out effect (HPS-salt) JCTC 2021.

Script for running the model in HOOMD-Blue.

Predicting scaling exponent of IDPs

A predictor of using both sequence charge (SCD) and hydrophobic (SHD) patterning parameters to estimate the scaling exponent of an IDP JCTC 2020.

Script

SAW-ν model

A self-avoiding walk polymer model with adjusted scaling exponent for interpreting the FRET data JCP 2018.

Script

Extended Guinier analysis

A model for interpreting Rg and scaling exponent of an IDP from its SAXS measurement JMB 2018.

Script

Transient interactions

Models for estimating fraction of transient interactions from 1) the distance distribution profiles of intrinsically disordered proteins JPCB 2023; or 2) the charge content of the sequence biorxiv 2025.

Github

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