The DegScore model is a ridge regression trained on Eterna Roll-Your-Own structure data to predict RNA degradation.

Citation: Leppek, K., Byeon, G.W., Kladwang, W., Wayment-Steele, H.K., Kerr, C., ... Barna, M., Das, R. (2021). Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics. https://www.biorxiv.org/content/10.1101/2021.03.29.437587v1.

If you find this code useful, please cite

Wayment-Steele, H., Kim., D.S. DegScore. (2022) Zenodo. https://doi.org/10.5281/zenodo.7130659

Setup:

Add to python path in .bashrc, or in python code with

sys.path.append('/path/to/DegScore')

Usage:

Example syntax:

from DegScore import DegScore

mdl = DegScore('GGGUUUCCC', structure='(((...)))')
print(mdl.degscore_by_position)
print(mdl.degscore)
print(mdl.est_half_life)

Output:

[0.17  0.217 0.511 0.641 0.714 0.49  0.347 0.15  0.643]
3.8830000000000013
11.430771365678682

Data Sources

Experiment	Data Repository
pH 10, Mg2+=10 mM, 24˚C, 1 day	https://rmdb.stanford.edu/detail/RYOS1_MGPH_0000
pH 10, Mg2+=0 mM, 24˚C, 7 days	https://rmdb.stanford.edu/detail/RYOS1_PH10_0000
pH 7.2, Mg2+=10 mM, 50˚C, 1 day	https://rmdb.stanford.edu/detail/RYOS1_MG50_0000
pH 7.2, Mg2+=0 mM, 50˚C, 7 days	https://rmdb.stanford.edu/detail/RYOS1_50C_0000
SHAPE structure mapping	https://rmdb.stanford.edu/detail/SHAPE_RYOS_0620

Kaggle competition for degradation prediction, which used the same training/test dataset: https://www.kaggle.com/c/stanford-covid-vaccine

To learn more

For more details on usage, and how degradation rate and half life are estimated from DegScore, see Demo/Degscore_demo.ipynb.

For code and data to reproduce a similar windowed Ridge regression model, see ReproduceDegscore/reproduce_degscore.ipynb. (Note fit is stochastic so coefficients cannot be reproduced exactly.)

Predicting secondary structure from DegScore class

If a secondary structure is not provided and Arnie is set up, DegScore can also calculate a secondary structure in place.

The default package is set to EternaFold, to be the same as the Eterna DegScore 2.1 calculation. This requires having successfully set up Arnie with EternaFold.

To change to other Arnie settings:

To use ViennaRNA (if set up):

mdl = DegScore(sequence, package='vienna', linear=False)

To use LinearFold-V (if set up):

mdl = DegScore(sequence, package='vienna', linear=True)