Parameters

Dictionary contains parameters for hps model. First level is the model name

HPS-Kr scale was taken from:

Dignon, G. L., Zheng, W., Kim, Y. C., Best, R. B., ; Mittal, J. (2018). Sequence determinants of protein phase behavior from a coarse-grained model. PLoS Computational Biology, 1–23. https://doi.org/10.1101/238170
Parameter for Nucleic acids (KR scale):

Regy, R. M., Dignon, G. L., Zheng, W., Kim, Y. C., Mittal, J. (2020). Sequence dependent phase separation of protein-polynucleotide mixtures elucidated using molecular simulations. Nucleic Acids Research, 48(22), 12593–12603. https://doi.org/10.1093/nar/gkaa1099

Phosphorylation version of some residues for KR scale are taken from:

Perdikari, T. M., Jovic, N., Dignon, G. L., Kim, Y. C., Fawzi, N. L., Mittal, J. (2021). A predictive coarse-grained model for position-specific effects of post-translational modifications. Biophysical Journal, 120(7), 1187–1197. https://doi.org/10.1016/j.bpj.2021.01.034

Note on hps (lambda) in urry scale:

# These parameters were shifted by 0.08 from original parameters directly.

in the original paper: Regy, R. M., Thompson, J., Kim, Y. C., ; Mittal, J. (2021). Improved coarse-grained model for studying sequence dependent phase separation of disordered proteins. Protein Science, 30(7), 1371–1379. https://doi.org/10.1002/pro.4094

..math::

lambda_{ij} = muy lambda_0_ij - delta

muy=1, delta= 0.08 is the optimal set for the set of 42 proteins they studied. lambda_{ij} = lambda0_{ij} - 0.08 = 0.5*(lambda_i+lambda_j) - 0.08 = 0.5(lambda_i -0.08 + lambda_j-0.08)

In both version, KR and Urry, we can tune directly lambda parameter in Urry by 0.08 so we can use only one equation for two model (choose parameter when passing model parameter)

hps.parameters.model_parameters.parameters: dictionary contains model parameters.